4.0003 and previous versions had a variety of bugs that would repeat.
Sounds like a typical case of you don't have "Display LUA errors" enabled, so you can't see all the repeating addon errors you are getting, which are killing your FPS.
Read this and enable it:
http://www.wowinterface.com/forums/s...ad.php?t=21817
Does it actually say 4.0006 in the chat window when you log into a character?
You could also see the version number in the addon list or C minimap button tooltip.
Remember to delete all the current Interface\AddOns\Carbonite folders before unzipping the new version, since the files may not always overwrite old ones.