[Xposed Framework Modules] Spere:
I got a problem here.

Scanner wont found some files from extsdcard.

I have "Directories" and "Media Types" enabled. Now this is strange I think.

I have .scanmedia file in these directories:

/storage/extSdCard/DCIM/

/storage/extSdCard/MyGalaxyNote/Sounds/

/storage/extSdCard/MyGalaxyNote/Pictures/

/storage/extSdCard/MyGalaxyNote/Music/

/storage/extSdCard/MyGalaxyNote/SGS II/

Why it scans only /DCIM/ and doesn't find marker file from those other directories?

Here is some log for you (took after: clearing log --> deleting media store contents --> trigger mediascanner):

XMSO: Intent Intent { act=com.thomashofmann.xposed.mediascanneroptimizer.DELETE_MEDIA_STORE_CONTENTS flg=0x10 } received.
XMSO: Request to delete MediaStore content
XMSO: Modified MediaStore.Files external volume URI is content://media/external/file?deletedata=false
XMSO: Deleted 1,418 rows from file entries
XMSO: createSimpleNotification with title Media Scanner Optimizer, text Deleted 1418 entries, subText null
XMSO: createSimpleNotification with title Deleted media store content., text null, subText null
XMSO: Intent Intent { act=com.thomashofmann.xposed.mediascanneroptimizer.SCAN_EXTERNAL flg=0x10 } received.
XMSO: Request to rescan external volume.
XMSO: onStartCommand is called with Intent Intent { cmp=com.android.providers.media/.MediaScannerService (has extras) }, startId 1, filepath null, mimetype null and volume external on com.android.providers.media.MediaScannerService@42c9a1d8
XMSO: startIdsByPid is {18995=1}
Reloaded preferences: {pref_prevent_repetetive_scans_state=true, pref_run_media_scanner_as_foreground_service_state=true, pref_restrict_directories_to_scan_state=true, pref_log_to_xposed_log_state=true, pref_show_results_state=true, pref_logging_enabled_state=true, pref_restrict_to_certain_media_types_state=true, pref_run_media_scanner_with_background_thread_priority_state=true}
XMSO: Number of start commands for external volume is 4
XMSO: Number of successful runs for external volume is 2
XMSO: scan is called for directories [/storage/emulated/0, /storage/extSdCard, /storage/UsbDriveA, /storage/UsbDriveB, /storage/UsbDriveC, /storage/UsbDriveD, /storage/UsbDriveE, /storage/UsbDriveF] on volume external
XMSO: Set service to foreground
XMSO: createSimpleNotification with title Media Scanner Optimizer, text Processing volume external, subText null
XMSO: Searching directories to scan in /storage/emulated/0
XMSO: Marker file exists in directory /storage/emulated/0/Ringtones
XMSO: Marker file exists in directory /storage/emulated/0/Download
XMSO: Marker file exists in directory /storage/emulated/0/DCIM
XMSO: Marker file exists in directory /storage/emulated/0/Bluetooth
XMSO: Marker file exists in directory /storage/emulated/0/Sounds
XMSO: Finished searching directories to scan in /storage/emulated/0. Time: 00:00
XMSO: Searching directories to scan in /storage/extSdCard
XMSO: Marker file exists in directory /storage/extSdCard/DCIM
XMSO: Finished searching directories to scan in /storage/extSdCard. Time: 00:00
XMSO: Searching directories to scan in /storage/UsbDriveA
XMSO: Finished searching directories to scan in /storage/UsbDriveA. Time: 00:00
XMSO: Searching directories to scan in /storage/UsbDriveB
XMSO: Finished searching directories to scan in /storage/UsbDriveB. Time: 00:00
XMSO: Searching directories to scan in /storage/UsbDriveC
XMSO: Finished searching directories to scan in /storage/UsbDriveC. Time: 00:00
XMSO: Searching directories to scan in /storage/UsbDriveD
XMSO: Finished searching directories to scan in /storage/UsbDriveD. Time: 00:00
XMSO: Searching directories to scan in /storage/UsbDriveE
XMSO: Finished searching directories to scan in /storage/UsbDriveE. Time: 00:00
XMSO: Searching directories to scan in /storage/UsbDriveF
XMSO: Finished searching directories to scan in /storage/UsbDriveF. Time: 00:00
XMSO: The following directories will be scanned by MediaScanner: [/storage/emulated/0/Ringtones, /storage/emulated/0/Download, /storage/emulated/0/DCIM, /storage/emulated/0/Bluetooth, /storage/emulated/0/Sounds, /storage/extSdCard/DCIM]
XMSO: Changing thread priority in MediaScanner constructor
XMSO: In android.media.MediaScanner#processDirectory prescan
XMSO: In android.media.MediaScanner#processDirectory beforeHookedMethod
XMSO: createSimpleNotification with title Media Scanner Optimizer, text Scanning /storage/emulated/0/Ringtones, subText null
XMSO: In android.media.MediaScanner#processDirectory beforeHookedMethod
XMSO: createSimpleNotification with title Media Scanner Optimizer, text Scanning /storage/emulated/0/Download, subText null
XMSO: In android.media.MediaScanner#processDirectory beforeHookedMethod
XMSO: createSimpleNotification with title Media Scanner Optimizer, text Scanning /storage/emulated/0/DCIM, subText null
XMSO: In android.media.MediaScanner#processDirectory beforeHookedMethod
XMSO: createSimpleNotification with title Media Scanner Optimizer, text Scanning /storage/emulated/0/Bluetooth, subText null
XMSO: In android.media.MediaScanner#processDirectory beforeHookedMethod
XMSO: createSimpleNotification with title Media Scanner Optimizer, text Scanning /storage/emulated/0/Sounds, subText null
XMSO: In android.media.MediaScanner#processDirectory beforeHookedMethod
XMSO: createSimpleNotification with title Media Scanner Optimizer, text Scanning /storage/extSdCard/DCIM, subText null
XMSO: In android.media.MediaScanner#processDirectory prescan
XMSO: createSimpleNotification with title Media Scanner Optimizer, text Postscan, subText null
XMSO: scan(String[] directories, String volumeName) has finished scanning external
XMSO: createBigTextStyleNotification with title Media Scanner Optimizer, text Scan directories time 00:14, subText Volume external (Expand for details), inboxSummary Volume external
XMSO: stopSelf is called on MediaScannerService
1133:run
XMSO: Received intent Intent { act=pref-xmso flg=0x10 }
XMSO: Reloading settings due to broadcast.
Reloaded preferences: {pref_prevent_repetetive_scans_state=true, pref_run_media_scanner_as_foreground_service_state=true, pref_restrict_directories_to_scan_state=true, pref_log_to_xposed_log_state=true, pref_show_results_state=true, pref_logging_enabled_state=true, pref_restrict_to_certain_media_types_state=true, pref_run_media_scanner_with_background_thread_priority_state=true}

Edit:

Galaxy Note 3 (SM-N9005)

Stock rooted TouchWiz 4.4.2 KitKat