Have you tried:
– deactivating all plugins to see if this resolves the problem? If this works, re-activate the plugins one by one until you find the problematic plugin(s).
– resetting the plugins folder by FTP or phpMyAdmin? Sometimes, an apparently inactive plugin can still cause problems.
I only had two plugins enabled. Disabled them and have the same problem.
Removed all plugins from the plugins folder and had the same problem.
Note that my main feed says:
Comments on: Mike’s Weblog which is strange enough and then my comments feed has:
The Kaply Korner » Page not found
Which means that somehow it’s picking up a page from my main site (kaply.com has a separate wordpress install)
I’m moving back to 2.8.6 for now.
Downgraded and my RSS feeds are still gone. DANG. They were working before I started this whole process…
Time for a fresh install.
OK, fresh install fixed it. Did feed URLs change with 2.9?
My old atom feed was:
http://www.kaply.com/weblog/feed/atom/
Which no longer works.
Now it is:
http://kaply.com/weblog/?feed=atom
So clearly I can’t go back in time, but it looks like the problem is that somehow the upgrade changed my permalinks settings.
That’s all I can come up with.
I switched my permalinks settings in my new install to month/day and everything is working as it used to.