Well all I can say is I have done the same update as you, have SB 3.5.1, firefox 2.0.0.4 installed in a non-default location and I don’t experience that problem.

The link you gave is 8 days old and only three posts of people that are effected, so it doesn’t appear to be that wide spread.

Have you tried the FEBE (Firefox Extension Backup Extension) which will backup your existing extensions and profiles if you wish, save it (backup data) to a different location. Then you can attempt a clean install of firefox, install the FEBE extension and see if SB recognises it and then try to restore the FEBE backup.