Sorry that you ended up reformatting to fix this. That's a sledgehammer approach to a surgical need, but without the know-how and with customer support being no help (some might say anti-helpful), sometimes the sledgehammer is faster and easier at the end of the day.
I had suggested to you that you search the registry to see what you could learn. Did you learn anything? Are other settings there? Do any of the settings point to other locations in the user profile than the ones that I mentioned? Did you try copying the whole working profile over the whole non-working profile? Vice versa? What effect did each copy have?
(I can't see how a 3rd party uninstaller would help here, but I've never used one.)
I don't know that this issue is the result of poor software design. *Every* software program comes with flaws, even the best ones. The difference in quality among software makers is in how much they test and fix before and after release. In this case, FTM was released too early (one might argue with known issues at that), and thereafter has been poorly supported, especially in cases like *this issue* where the support crew runs interference for the developers who are disconnected from the community with a small number of individual exceptions. If one of the developers knew that FTM would sync or run from one profile and not another, then my guess is that we'd very quickly get a list of potential causes.