Actually, I agree with you that the problem is an errant installer. The installer at fault is the Soyo Bay One driver disk. I have installed/uninstalled a number of times to verify this.
Unfortunately I NEED this to get my Bay One to work... (although it's not working now). There are no options for WHERE to install, and because of the typical problems you mentioned, I ALMOST always allow the installation program to install in the directory it wants. The only exception I make to that rule is anything to be installed to the root directory... I won't allow that.
If I had to guess, I'd say the installer is overriding the Windows "flag" that directs Windows to either start with the previously open folders, or not. If I can find where in the Registry that flag is located, perhaps I can verify/fix that. Can anyone point me to that location in the Registry???