I don't have an real answer for you, but it's also a problem I've encountered without even using Troubleshooter 2.
I have 2 Aimtrak based guns (Arcade Guns) hooked up to my cabinet using an Windows 7 64 bit machine.
Every so often the IDs for the guns (hooked up via USB) will change. It will almost always happen if I plug in a flash drive or something else for maintenance/data upload to my cabinet.
Rather than constantly reconfiguring the settings for the IDs in MAME, Demul, Sega M2 and Supermodel on my cabinet over and over again, I just reboot the system and cross my fingers. Usually within a reboot or two the IDs go back to the original settings I expected.
Maybe that will help you?
If anyone else knows how to keep the ID settings in Windows 7 the same no matter what, I'd love to know as well.