You've posted some code which removes autofilters. I can only guess that this is the code that fails to REMOVE some dropdown buttons - at the moment, only you know. I've been suggesting that the arrows are not there to have to remove in the first place (by doing that we don't later have to have a separate routine to rout out those errant buttons and selectively delete them while at the same time not upsetting any other buttons).
In post #6 I talked about the Autofilter method - I still haven't seen such code (do a search for the likes of Autofilter with the Find whole words only box checked - there'll probably be several instances).
All your reiteration of books calling macros is of no value unless I can see the code.
If this code is much too long, then only send snippets including any lines which add or change autofilters to sheets, and perhaps a few lines before so I have a clue what sheet it's working on, and perhaps a few lines after for context. Worst case: place a version of your file(s) on the interweb - box.net, skydrive, whatever.
I have a possible solution probably consisting of adding VisibleDropdown:=False in one or more places (short, simple and robust). You seem to pass over it without saying why.
Is it because the dropdowns need to be manipulated on the sheet by a user? I haven't the foggiest.
We are dealing with Excel misbehaving - you're trying to solve it with sticking plaster, I'm hoping to remove the need for sticking plaster.