I should mention first - we don't yet have support for n64 or gamecube, so if you're testing those ROMs, they won't show. Also, note that we don't yet have sorting or categorization setup, so for now the games display sorted first by platform (steam, arcade, nes, etc), and then alphabetically.
Can you list for us a few filepath examples of ROMs that are not showing up for you? For example:
C:\Users\Flynn\AppData\Roaming\polycade\games\arcade\asteroid1.zip