[Eee Pad Transformer Q&A, Help & Troubleshooting] RuntimeErr:
When installing with option 3 (linux only) I get this message.

reading config file ./boot/purelinux.cfg
reading kernel from ./kernels/2636-zImage
reading ramdisk from ./kernels/initrd-2.6.36.img
Writing Boot Image ./tmp/linux.img
Put your device in APX mode then press any key
Device detected in APX mode
Nvflash started
[B]nvflash configuration file error: partition/ filesystem_type invalid[/B]
Device needs to be put back into APX mode
Putting device into Nv3P Phone Update mode
Nvflash started
nvflash configuration file error: file not found
Nvflash started
[resume mode]

It may be a typo in the config file on line 85 of config/linux.cfg by changing ext3c to ext3.

80 [partition]
81 name=UBT
82 id=8
83 type=data
84 allocation_policy=sequential
[B] 85 filesystem_type=ext3c[/B]
86 size=554720302
87 file_system_attribute=0
88 partition_attribute=0
89 allocation_attribute=0x808
90 percent_reserved=0

After fixing it by changing ext3c to ext3 I get this:

reading config file ./boot/purelinux.cfg
reading kernel from ./kernels/2636-zImage
reading ramdisk from ./kernels/initrd-2.6.36.img
Writing Boot Image ./tmp/linux.img
Put your device in APX mode then press any key
Device detected in APX mode
Nvflash started
rcm version 0X20001
System Information:
chip name: t20
chip id: 0x20 major: 1 minor: 3
chip sku: 0x8
chip uid: 0x0364804443605257
macrovision: disabled
hdcp: enabled
sbk burned: true
dk burned: true
boot device: emmc
operating mode: 4
device config strap: 0
device config fuse: 0
sdram config strap: 0

sending file: ./images/transformer.bct
- 4080/4080 bytes sent
./images/transformer.bct sent successfully
odm data: 0x300d8011
downloading bootloader -- load address: 0x108000 entry point: 0x108000
sending file: ./images/bootloader.bin
| 976013/976013 bytes sent
./images/bootloader.bin sent successfully
waiting for bootloader to initialize
bootloader downloaded successfully
setting device: 2 3
creating partition: BCT
creating partition: PT
creating partition: EBT
creating partition: SOS
creating partition: LNX
creating partition: GP1
creating partition: UBT
creating partition: PAD
creating partition: PA2
creating partition: USP
creating partition: GPT
Formatting partition 2 BCT please wait.. done!
Formatting partition 3 PT please wait.. done!
Formatting partition 4 EBT please wait.. done!
Formatting partition 5 SOS please wait.. done!
Formatting partition 6 LNX please wait.. done!
Formatting partition 7 GP1 please wait.. done!
Formatting partition 8 UBT please wait.. done!
Formatting partition 9 PAD please wait.. done!
Formatting partition 10 PA2 please wait.. done!
Formatting partition 11 USP please wait.. done!
Formatting partition 12 GPT please wait.. done!
done!
sending file: ./images/bootloader.bin
| 976013/976013 bytes sent
./images/bootloader.bin sent successfully
sending file: ./images/recovery.img
- 4499456/4499456 bytes sent
./images/recovery.img sent successfully
sending file: ./images/boot.img
/ 3618816/3618816 bytes sent
./images/boot.img sent successfully
Device needs to be put back into APX mode
Putting device into Nv3P Phone Update mode
Nvflash started
[B]nvflash configuration file error: file not found[/B]
Nvflash started
[resume mode]
[B]connection failed NvError 0x8[/B]

Which I fixed by editing line 11 of scripts/flash.sh from:

8 Nv3P_Server() {
9
10 echo "Putting device into Nv3P Phone Update mode"
11 ./bins/nvflash --bct ./images/transformer.bct --setbct [B]--configfile ./configs/$LAYOUT.cfg[/B] --bl ./images/bootloader.bin --odmdata $ODMDATA --sbk $SBK --sync
12
13 }

to

8 Nv3P_Server() {
9
10 echo "Putting device into Nv3P Phone Update mode"
11 ./bins/nvflash --bct ./images/transformer.bct --setbct [B]--configfile ./configs/$LAYOUT[/B] --bl ./images/bootloader.bin --odmdata $ODMDATA --sbk $SBK --sync
12
13 }

And in the end when it finished correctly it just loads the main boot screen and freezes.

Please check if the scripts are correct (and if it actually works if you can).