The most important thing about installing FT3 (and CC3, but not CC3+) is that you install it into a location other than Program Files (or Program Files (x86)). Windows believes that only administrators should be able to modify the contents of those directories. FT3 believes that it is perfectly acceptable for it to store information in its own install directory. As you might expect in this war of the wills, Windows wins and FT3 won't properly save its updated information. I've had some discussions with it and it's considering mending its ways, but for now your best bet for a good experience is to just avoid installing to the Program Files place in the first place.

The issues with the start menu operation are probably due to the installer keeping you safe (or maybe Windows is keeping you safe: it's hard to be sure sometimes).

I am glad to hear that things have resolved themselves.