For security reasons, I deleted your previous PM containing the password for the .htaccess protection on the AdminCP. Could you please re-send that information?
Update: Sorry for the delay on this. This was actually technically not a bug - the drop-down excluded all categories where users did not have permission to upload files.
However, I recognise that with a complex setup such as yours, this can get extremely confusing. For that reason, I have updated the drop-down menu to simply disallow selection of categories that would otherwise be hidden, and patched your site with this change.
You should now find that the drop-down display makes much more sense