Hi Mike,
The newest version of FCKeditor has some fixes for some Firefox 3 issues. I've already upgraded to this version in svn trunk so it will be in the next release.
Hopefully this includes the fix for the paste as word issue.It does say something about fixing some bug in the cleanup logic which I think means the html cleaning they do for things pasted in.
I'm not a big fan of pasting from Word. Word makes notoriously nasty markup and I don't have enough confidence in any cleanup process. I know you are doing it for color coded code samples, but my concern would be whether the resulting page would pass the w3c validator after pasting content from Word.
Best,
Joe