A normal scan on a (more or less) modern drive usually takes (depens a bit on the sha1 settings) just a couple of minutes, so yes, something is wrong...
I'd go with a clean install (so all default options are set) and then simply do a scan without any fix options enabled. That should also be pretty fast and you already get an impression what is wrong with your collection. If too much appears, you may even have setup wrong rompaths...or a wrong merge mode (and fixing tries to recreate all the sets...). So checking the first non-fix scan would be a good idea to see if something is totally wrong configuration wise.
After that you should add missing stuff with the rebuilder and not via fix-missing (so keep that disabled).
Solid 7z archives may become a problem as soon as write operations are done on them since it would require a complete recompression of the files.
3rd party tools like virusscanner can interfear. If you're using a network drive, bad configurations can cause slow downs...even bad drivers can do.
A soon dying harddisk can also be a slow down factor....but don't worry...pretty rare case...
....and sure I recommend to use an official MAME import, no softwarelists, split sets and zipfile usage