I just upgraded today from version 1.01 to 2.01. No problems to speak of. I've got a battery grip, which needs to be removed and use the battery in the camera itself at least according to Nikon since there may be the potential the firmware upgrade may have changes to the MB grip itself.
Seems to me that the instructions for the firmware upgrade answer your question. Here's what it says:
Check the current camera firmware version 1 Turn the camera on. 2 Press the MENU button and select Firmware Version in the setup menu. * Illustration shows dialog displayed when both A and B firmware have been updated to version 2.00 or later. 3 Two firmware versions (A and B) will be displayed. Both should be earlier than 2.00. 4 Turn the camera off.
Doesn't number THREE cover your situation?
I'm also not sure how you are contacting Nikon, but I have found that using the Knowledgebase Q&A system works wonders. Turnaround time is less than a day, in most cases.
Joseph is right - there are usually undocumented fixes in firmware updates. I generally try to keep my firmware completely current. Any bugs are normally identified within a few days of the firmware release.