MU plugins not upgrading

I had a pre 3.x version of MU installed and as I can recall, since the original installation, the plugins won’t upgrade. I can go through the upgrade process via the web and it appears to be successful but when the page refreshes, it shows it still needs to be upgraded. I just upgraded to 3.0.1 and I’m having the same problem. I’ve now got 8 plugins that need to be upgraded. I haven’t tried manual as I’m sure that will work but is only a bandaid and I’d like to resolve the web driven upgrade problem. My file system is owned by the FTP user and the chmod is 777 (I know, overkill). Suggestions?