Hi Joe,
Seeing your other message on your upgrade, one of the more non-obvious changes is that there's an additional <div class="dokuwiki"> that might fix some of the problems you're having... and in fact is required for some plugins to work properly. (Your mileage may vary.)
The only two things that leaped out at me that had a change was the style information for TOC (which you mentioned) and spell checker... both had the additional underscores added to them.
Also, for resolving any remaining issues, might I suggest this since you said you're using FireFox:
http://chrispederick.com/work/webdeveloper/
After installing it, choose "view style information", and anything you mouse over will give its complete CSS hierarchy or information and may give you an opportunity to fix things faster as you can address them right away.
Good luck, -- --Terence J. Grant(tjgrant@xxxxxxxxxxxx) -- DokuWiki mailing list - more info at http://wiki.splitbrain.org/wiki:mailinglist