Mystery of missing files

[user11]

The setup:
POGO B04 arch on flash stick, media files on EXT3 HDD, SAMBA streaming media files to Raspberri Pi running Open Elec

The problem:
After watching some of those files I decided to move them to another folder on the same drive.
Surprisingly a few of those big media filse were missing when browsed under windows SAMBA share. I've logged on and listed all files using ls -a command. Still no luck. Most of the files are present, but some are missing. Rebooted both - Pogo and Pi. No change. Checked disc using Ubuntu laptop and gparted - no errors found, files still missing. I can't see those files under Arch, but I can see them when browsing through Pi - and I can play them! Any explanation?