I have the same issue, using Office 2008, 10.6.4. It looks like it could be some script cleaning things up because, during that "quit period", all the Excel menu bar items *except* for the script menu disappear. Cleaning up what I don't know. It is a bit annoying.
Thanks for confirming that I'm not alone.
I'm also running Office 2008 in OS X 10.6.4, I've installed the update MS said I needed, and I even reinstalled Excel...all with no joy.
In my case, though, the entire menu bar remains intact while Excel does something
very processor intensive before it quits.
It's more than just "a bit" annoying!
Edit: And it's not like I'm quitting huge files; one is 25Kb and the other is 145Kb.