The internal drive does seem to be formatted differently. Via the XMB, I can access and play large files ( > 4gb ) on the internal 160gb drive with no trouble. The PS3 formatted the internal drive on first power on after I put it in, it looks like that file system is more large file friendly. That makes sense since it would have to be if Sony ever decided to start offering downloadable HD movies.
Getting on my soapbox for a second, I really do hope they address this problem with external drives one day. It's frustrating that both of these consoles (360/PS3) could make amazing media players, but they always seem hobbled with a variety of limitations that get in the way ;( I'm starting to think neither will ever beat a PC for being a media machine because of the self imposed limitations they each seem to have. In other words, maybe Sony will never support stuff like NTFS or WMV, or maybe Microsoft will never support DivX, MOV, etc... It's particularly frustrating with the PS3, since that machine has the potential to be the ultimate home media machine.