When I upgraded, I was installing the new version on a PC and a laptop, plus portably onto an external drive and a NAS.
I found that once installed, and MM was open, it wouldn't have my previous skins etc. I just had to shut MM down and open it back up in order for it to pick up those previous settings. And when installing portably, I made the mistake of installing into a new subdirectory of my MM folder, instead of into the MM folder itself. That puzzled me until I spotted my error.
Other than that, I had no problems. So I'd suggest double-checking the location of your installation, your previous ini file, etc. You may find, on closer examination, that things are not where you thought they were.
I always have a backup of ini files as well as db files, just in case.