I think I might have discovered the problem.

I have a folder named "roms", in that folder I have standard roms(that don't need a BIOS).
In the "roms" folder there are other folders for roms that require a BIOS such as NEO-GEO, PlayChoice10, etc...

My mame.ini file has the following line:

rompath "roms;roms\Neo-Geo;roms\PlayChoice10;(etc...)

So, in clrmameplus settings when I click the "Import" button to import the rom paths from the mame.ini file, all paths are imported except the first one "roms".
That's why only some roms are showing up in the have/miss lists.

After manually adding the "roms" folder, the lists are working now.

Thanks