I just had the strangest experience transforming my data from a Windows Home Server to a Linux Based fileserver.

Situation:
2 HDD, both SATA, both NTFS so I'm faced with the task of converting them to ext4 and not enough storage space to keep two copies of everything

After some research I decide to create an ext4 partition, fill it up using a Ubuntu live CD (so files never leave the drive, just copied from NTFS partition to ext4 partition), and then using GParted shrink the NTFS partition smaller, add the free space to the ext4 partition and copy some new files in the same way as above. In the end I have to fully ext4 drives.

And then the problem: a lot of my video files now seem corrupt. I can play them all (all types of formats mkv, avi, DVDs) but after a few minutes of playing all programs shut off.

So the seek index of all these files seems corrupted somehow.
Some further investigations: a typical file is 1.66 GB in Windows NTFS and is now only 1.1 GB in ext4. However this seems normal since even working files are 1.1 GB.

And after some further research only the files come from drive 1 are corrupt, the other files from drive 2 play just fine and they were copied in the same manner.

So to sum up:

-only video files from drive 1 are affected (music and photos are fine)
-file sizes seem correct, approximately the same as the files from drive 2

Questions: What could have caused this kind of behaviour? Both drive were exactly the same and treated the same.

Secondly: is there a way to repair the mkv files? AVI files seem repairable, however all my searches for an mkv repair tool have pointed to project Meteorite (meteorite.sourceforge.net/) which just doesn't work for me (neither on Windows or Linux)

Thanks