Permalink Problems with Wordpress 2.5

So I’ve got several different sites running on Wordpress and about a week ago I started upgrading all of them to version 2.5.  I really like the upgrade so far, the admin interface is taking a little bit to get used to but overall I really like it.   Now all of my sites seem to be doing fine with the upgrade with the exception of one that I noticed was having massive permalink problems.

This is actually site running of the popular wordpress ebay plugin called PhpBay and I highly recommend it for building some great niche ebay sites to make some cash.  It’s the best $49 that I’ve spent in awhile to generated some solid profits.

So I’ve got a few sites running this plugin but only one seems to be having problems with the permalink structure.  I’m really not sure what the issue is because some of the permalinks work and others that should be working are pointing to 404 errors that the post is not there.  In addition I’ve got lots of other plugins running as well and I’ve made sure they’re all compatible with 2.5, disabled them, and nothing seems to fix the problem.  At this point I’m probably going to restructure the whole site anyway to take advantage of some SEO stuff that I overlooked the first time around, but this is still very frustrating because I cannot figure out what seems to be causing this.

If anyone else has had any problems like this I’d definitely love to hear the solution that you’ve come up with.  I’m honestly just thinking that something crazy happened during the upgrade since this is the only site that it happened on.