[Android Software Development] mattmanwrx:
You got your own folder on my desktop ;)

anyways, it all built fine for me (apart from translation warnings)...

C:\Users\Webmaster\Desktop\apktool\groovy>apktool d -t groovy Rosie.apk
I: Loading resource table...
I: Loaded.
I: Decoding AndroidManifest.xml with resources...
I: Loading resource table from file: C:\Users\Webmaster\apktool\framework\1-groovy.apk
I: Loaded.
I: Loading resource table from file: C:\Users\Webmaster\apktool\framework\2-groovy.apk
W: Config flags size > 36. Exceeding bytes: 0x2000000.
W: Invalid config flags detected: dimen-mdpi-ERR0
W: Config flags size > 36. Exceeding bytes: 0x4000000.
W: Invalid config flags detected: dimen-mdpi-ERR1
W: Config flags size > 36. Exceeding bytes: 0x5000000.
W: Invalid config flags detected: dimen-mdpi-ERR2
W: Config flags size > 36. Exceeding bytes: 0x6000000.
W: Invalid config flags detected: dimen-mdpi-ERR3
W: Config flags size > 36. Exceeding bytes: 0x2000000.
W: Invalid config flags detected: dimen-hdpi-ERR4
W: Config flags size > 36. Exceeding bytes: 0x4000000.
W: Invalid config flags detected: dimen-hdpi-ERR5
W: Config flags size > 36. Exceeding bytes: 0x5000000.
W: Invalid config flags detected: dimen-hdpi-ERR6
W: Config flags size > 36. Exceeding bytes: 0x6000000.
W: Invalid config flags detected: dimen-hdpi-ERR7
W: Config flags size > 36. Exceeding bytes: 0x2000000.
W: Invalid config flags detected: dimen-xhdpi-ERR8
W: Config flags size > 36. Exceeding bytes: 0x4000000.
W: Invalid config flags detected: dimen-xhdpi-ERR9
W: Config flags size > 36. Exceeding bytes: 0x5000000.
W: Invalid config flags detected: dimen-xhdpi-ERR10
W: Config flags size > 36. Exceeding bytes: 0x6000000.
W: Invalid config flags detected: dimen-xhdpi-ERR11
W: Config flags size > 36. Exceeding bytes: 0x2000000.
W: Invalid config flags detected: dimen-ja-mdpi-ERR12
W: Config flags size > 36. Exceeding bytes: 0x4000000.
W: Invalid config flags detected: dimen-ja-mdpi-ERR13
W: Config flags size > 36. Exceeding bytes: 0x5000000.
W: Invalid config flags detected: dimen-ja-mdpi-ERR14
W: Config flags size > 36. Exceeding bytes: 0x2000000.
W: Invalid config flags detected: dimen-ja-hdpi-ERR15
W: Config flags size > 36. Exceeding bytes: 0x4000000.
W: Invalid config flags detected: dimen-ja-hdpi-ERR16
W: Config flags size > 36. Exceeding bytes: 0x5000000.
W: Invalid config flags detected: dimen-ja-hdpi-ERR17
W: Config flags size > 36. Exceeding bytes: 0x2000000.
W: Invalid config flags detected: dimen-ja-xhdpi-ERR18
W: Config flags size > 36. Exceeding bytes: 0x4000000.
W: Invalid config flags detected: dimen-ja-xhdpi-ERR19
W: Config flags size > 36. Exceeding bytes: 0x5000000.
W: Invalid config flags detected: dimen-ja-xhdpi-ERR20
W: Config flags size > 36. Exceeding bytes: 0x2000000.
W: Invalid config flags detected: dimen-ko-mdpi-ERR21
W: Config flags size > 36. Exceeding bytes: 0x4000000.
W: Invalid config flags detected: dimen-ko-mdpi-ERR22
W: Config flags size > 36. Exceeding bytes: 0x5000000.
W: Invalid config flags detected: dimen-ko-mdpi-ERR23
W: Config flags size > 36. Exceeding bytes: 0x2000000.
W: Invalid config flags detected: dimen-ko-hdpi-ERR24
W: Config flags size > 36. Exceeding bytes: 0x4000000.
W: Invalid config flags detected: dimen-ko-hdpi-ERR25
W: Config flags size > 36. Exceeding bytes: 0x5000000.
W: Invalid config flags detected: dimen-ko-hdpi-ERR26
W: Config flags size > 36. Exceeding bytes: 0x2000000.
W: Invalid config flags detected: dimen-ko-xhdpi-ERR27
W: Config flags size > 36. Exceeding bytes: 0x4000000.
W: Invalid config flags detected: dimen-ko-xhdpi-ERR28
W: Config flags size > 36. Exceeding bytes: 0x5000000.
W: Invalid config flags detected: dimen-ko-xhdpi-ERR29
W: Config flags size > 36. Exceeding bytes: 0x2000000.
W: Invalid config flags detected: dimen-zh-rCN-mdpi-ERR30
W: Config flags size > 36. Exceeding bytes: 0x4000000.
W: Invalid config flags detected: dimen-zh-rCN-mdpi-ERR31
W: Config flags size > 36. Exceeding bytes: 0x5000000.
W: Invalid config flags detected: dimen-zh-rCN-mdpi-ERR32
W: Config flags size > 36. Exceeding bytes: 0x2000000.
W: Invalid config flags detected: dimen-zh-rCN-hdpi-ERR33
W: Config flags size > 36. Exceeding bytes: 0x4000000.
W: Invalid config flags detected: dimen-zh-rCN-hdpi-ERR34
W: Config flags size > 36. Exceeding bytes: 0x5000000.
W: Invalid config flags detected: dimen-zh-rCN-hdpi-ERR35
W: Config flags size > 36. Exceeding bytes: 0x2000000.
W: Invalid config flags detected: dimen-zh-rCN-xhdpi-ERR36
W: Config flags size > 36. Exceeding bytes: 0x4000000.
W: Invalid config flags detected: dimen-zh-rCN-xhdpi-ERR37
W: Config flags size > 36. Exceeding bytes: 0x5000000.
W: Invalid config flags detected: dimen-zh-rCN-xhdpi-ERR38
W: Config flags size > 36. Exceeding bytes: 0x2000000.
W: Invalid config flags detected: dimen-zh-rTW-mdpi-ERR39
W: Config flags size > 36. Exceeding bytes: 0x4000000.
W: Invalid config flags detected: dimen-zh-rTW-mdpi-ERR40
W: Config flags size > 36. Exceeding bytes: 0x5000000.
W: Invalid config flags detected: dimen-zh-rTW-mdpi-ERR41
W: Config flags size > 36. Exceeding bytes: 0x2000000.
W: Invalid config flags detected: dimen-zh-rTW-hdpi-ERR42
W: Config flags size > 36. Exceeding bytes: 0x4000000.
W: Invalid config flags detected: dimen-zh-rTW-hdpi-ERR43
W: Config flags size > 36. Exceeding bytes: 0x5000000.
W: Invalid config flags detected: dimen-zh-rTW-hdpi-ERR44
W: Config flags size > 36. Exceeding bytes: 0x2000000.
W: Invalid config flags detected: dimen-zh-rTW-xhdpi-ERR45
W: Config flags size > 36. Exceeding bytes: 0x4000000.
W: Invalid config flags detected: dimen-zh-rTW-xhdpi-ERR46
W: Config flags size > 36. Exceeding bytes: 0x5000000.
W: Invalid config flags detected: dimen-zh-rTW-xhdpi-ERR47
W: Config flags size > 36. Exceeding bytes: 0x2000000.
W: Invalid config flags detected: integer-mdpi-ERR48
W: Config flags size > 36. Exceeding bytes: 0x4000000.
W: Invalid config flags detected: integer-mdpi-ERR49
W: Config flags size > 36. Exceeding bytes: 0x5000000.
W: Invalid config flags detected: integer-mdpi-ERR50
W: Config flags size > 36. Exceeding bytes: 0x6000000.
W: Invalid config flags detected: integer-mdpi-ERR51
W: Config flags size > 36. Exceeding bytes: 0x2000000.
W: Invalid config flags detected: integer-hdpi-ERR52
W: Config flags size > 36. Exceeding bytes: 0x4000000.
W: Invalid config flags detected: integer-hdpi-ERR53
W: Config flags size > 36. Exceeding bytes: 0x5000000.
W: Invalid config flags detected: integer-hdpi-ERR54
W: Config flags size > 36. Exceeding bytes: 0x6000000.
W: Invalid config flags detected: integer-hdpi-ERR55
W: Config flags size > 36. Exceeding bytes: 0x2000000.
W: Invalid config flags detected: integer-xhdpi-ERR56
W: Config flags size > 36. Exceeding bytes: 0x4000000.
W: Invalid config flags detected: integer-xhdpi-ERR57
W: Config flags size > 36. Exceeding bytes: 0x5000000.
W: Invalid config flags detected: integer-xhdpi-ERR58
W: Config flags size > 36. Exceeding bytes: 0x6000000.
W: Invalid config flags detected: integer-xhdpi-ERR59
I: Loaded.
I: Decoding file-resources...
I: Decoding values */* XMLs...
I: Done.
I: Copying assets and libs...

C:\Users\Webmaster\Desktop\apktool\groovy>apktool b Rosie
W: Could not find sources
I: Checking whether resources has changed...
I: Building resources...
aapt: warning: string 'all_apps_home_button_label' has no default translation in C:\Users\Webmaster\Desktop\apktool\groovy\Rosie\res; found: ca rm tl
aapt: warning: string 'all_apps_tab_all' has no default translation in C:\Users\Webmaster\Desktop\apktool\groovy\Rosie\res; found: ca tl
aapt: warning: string 'cancel_action' has no default translation in C:\Users\Webmaster\Desktop\apktool\groovy\Rosie\res; found: ca rm tl
aapt: warning: string 'delete_zone_label_all_apps' has no default translation in C:\Users\Webmaster\Desktop\apktool\groovy\Rosie\res; found: ca tl
aapt: warning: string 'delete_zone_label_workspace' has no default translation in C:\Users\Webmaster\Desktop\apktool\groovy\Rosie\res; found: ca tl
aapt: warning: string 'group_applications' has no default translation in C:\Users\Webmaster\Desktop\apktool\groovy\Rosie\res; found: ca rm tl
aapt: warning: string 'menu_add' has no default translation in C:\Users\Webmaster\Desktop\apktool\groovy\Rosie\res; found: ca rm tl
aapt: warning: string 'menu_notifications' has no default translation in C:\Users\Webmaster\Desktop\apktool\groovy\Rosie\res; found: ca rm tl
aapt: warning: string 'menu_search' has no default translation in C:\Users\Webmaster\Desktop\apktool\groovy\Rosie\res; found: ca rm tl
aapt: warning: string 'menu_settings' has no default translation in C:\Users\Webmaster\Desktop\apktool\groovy\Rosie\res; found: ca rm tl
aapt: warning: string 'menu_wallpaper' has no default translation in C:\Users\Webmaster\Desktop\apktool\groovy\Rosie\res; found: ca rm tl
aapt: warning: string 'rename_action' has no default translation in C:\Users\Webmaster\Desktop\apktool\groovy\Rosie\res; found: ca rm tl
I: Building apk file...

C:\Users\Webmaster\Desktop\apktool\groovy>

Firstly, these;

W: Config flags size > 36. Exceeding bytes: 0x2000000.
W: Invalid config flags detected: dimen-mdpi-ERR0

Are warnings - hence the "W" - warnings are just that, warning you that it could cause errors, but it doesn't!

Now for your actual problem, it could be an old aapt you're using? I've attached the one I've got (from the SDK Tools Revision 20 (I haven't upadted to 20.0.1)) and see if that works... :)

EDIT: Uploaded it in a .rar as XDA won't allow uploads of .exe files (rightly so :))