It doesn't sound like the Post Revisions problem, but anyway, you know about disabling post revisions to make Podpress work better in WP 2.6+, right? You could try that if you haven't done it yet.
I've seen the Duration detection problem a few times lately. Have not heard of a fix yet. But I have found that iTunes and the embedded player still work (for me) even on the episodes that have generic wrong 1:01 for duration.
I dunno about WMA, never tried with that, I'd stick with mp3 for testing (might not make any difference but anyway).
I came up with 2 ideas to further test yours. One is link Podpress to some external mp3 that you Know-know-know is a working mp3 on another server. For example find an mp3 on Archive.org the free internet library, and try podpressing that. Second idea is install a secondary mp3 player plugin - namely this one,
http://www.taragana.com/products/free-wordpress-plugins/mp3-player
It's super easy to install and works instantly on your direct mp3 links in your posts. It actually can work compatible with Podpress (altho you usually wouldn't need both, I have both on one site).
The point of installing the 2nd plugin is, see if your mp3 plays on that player. If it doesn't, there's something wrong with your mp3 or server. If it does play, then there's something messed in podpress.
hope this helps you diagnose
jsmith2482@yahoo.com
Dgold