So, we have established that the files are not being misinterpreted by your players and that they are not damaged.
I guess that takes us to your server software and the transmission process?
Have you updated anything on the server and have you checked to see if there is a more recent version of your RAID software and Openfiler, also have you tried fresh installations?
I am curious:
1. Does this only happen with episodes of the same show, and does it happen with all of them?
2. Otherwise does it happen with all shows from the same source?
Also do the shows freeze/hang or do they appear to terminate normally, albeit prematurely?
I am still toying with the possibility that there is something included in the file that is getting misinterpreted by your server.
Two things you might try:
1. Convert/copy one of the problem files to a different format
2. Resample one of the files that has the problem
Incidentally, does Openfiler produce any logs?