I have also had problems with NTFS partitions. My PBO Firmware was originally P020P02, and I updated it with the official B18 revisions as they came out.
After a few months I started to noticed issues related to corrupted files.
I reformatted/repartitioned my HDD using instructions provided by Snappy elsewhere in this forum.
That worked quite well for some time. I certainly noticed a big speed improvement whether it was previewing/starting up a video, or transferring files over the network or USB, and I never encountered file corruption. But I had occasional problems mounting the EXT3 partition in Samba that would require rebooting, or Telnet'ing to the console to restart Samba once the partition was mounted.
Then I flashed my PBO with the latest Medebo image, and decided to give NTFS a try again - formatting through the GUI. This time it only took a few weeks before I started noticing files that couldn't be removed. I suspect it has to do with the features in Medebo that weren't in the standard PBO firmware - like the jukebox, skins, and the video wall, and my frequent use of Y2M.
I plugged my PBO directly into my PC, and checked it using chkdsk. It found tons of errors.
So here I go again - pulling all of the data off my 500GB HDD so I can reformat it to EXT3 before putting all that data back on. Hopefully I can do it in a way that I won't have Samba problems the way I did before.
One question: Why don't media players like the PBO automatically perform disk maintenance on boot up, or on some regular schedule? Given the way in which the PBO/Medebo seems to trash the internal HDD, I think it would be a standard feature.
Once I get my disk re-imaged I plan on seeing if I can add fsck to cron… I guess that would require unmounting the volume first, which would require stopping Samba and Transmission… and then restarting it all afterwards. Fun, fun, fun!
Wish me luck!