I too have the same issue. It's only been in the last couple of months though. I tried upgrading my Java (now onto version 7, Update 10), my version of PS3 Media Server (1.72) and I still have the problems where the audio will stay at the constant speed, but the video just speeds up for no reason. I believe it's going through memcoder (which I've set to default) but even trying to use AviSynth/Memcoder has the same issues, or FFmpg doesn't even play the file.
If however, I stop the file, and re-enter the file (which takes me back to the start) and press the Square button, I can go back to that point in the file and it's ok for a bit, but then I have the same problem again.
The traces log shows no errors at all to indicate what's going on. I can post a debug log if that helps.
I am running Windows 7 x64 Professional, 8GB of RAM, Core 2 Duo E7400 @ 2.8Ghz. Wired 1GB connection to the PS3, even though PS3 Media Server reports it as 512Mb/s. I've set both the PS3 and NIC to 1GB Full Duplex, but 512Mb/s should be more that enough to network bandwidth to prevent this issue.
I think it's got something to do with either AC3 or AAC audio, because I was comparing two video files I downloaded using the Media Info application recommended off the bug page and the one that works has both an AC3 and a AAC audio stream, and the one that has the audio glitch only has the AAC.
If anyone has any suggestions, that would be great. I've had a look around, and I can't really find anything that matches, other than this thread!
EDIT: I tried unchecking the "Keep AC-3 track" option under common encode. Didn't make any change.