I can not speak for the issues you have with Vista(ster) [sorry, but I can not resist!!!

]; as I am an XP user.
I do not install ANY of my applications in %ProgramFiles% because, I knew someone who had his %ProgramFiles% sector on the disk get flaky, and of course, he did not back up the hard drive.

I am not about to let that happen to me. I install applications in 3 separate folders, one called APPS (that is where I hide Firefox and Thunderbird amongst others. The other folder is called TOOLS; I think what goes there is obvious (it is where I hide wireshark). The third folder is called ZANGO, (named after the infamous purveyor of malware); and that is where I hide Spybot S&D, my firewall, AdAware, etc. I have seen so many people's computers with a ton of folders in %ProgramFiles%; to me a disaster waiting to strike.
I have found that other extensions (but apparently not themes) are also subject to this behavior. I have decided to keep a list of them in the same folder as the scripts that are used to globally install extensions. Each time one of them is updated, I guess its uninstall, restart, and finally install the update. I hate this workaround, and it does not make my life any easier. But then again, who said that working with computers would be easy. I should have realized a long time ago (1970) that computers are indeed quirky. That lesson was trying to figure out why two names in a sorted list were out of sequence in a FORTRAN class project.
I am not sure if there is going to be a fix for this.

From what I have seen, global installs are at the bottom of the Mozilla dev teams priority lists. And that is shame, because, it may very well be one reason why corporate adoption of Firefox lags.
(Side note, I ran this through a spell checker, and the suggested replacement for "Mozilla" was 'Godzilla').

Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.9.0.10) Gecko/2009042316 Firefox/3.0.10