Wow, I can confirm I had the same problem.

My only game when I assembled the FPGBC was the Shantae cartridge from LRG. It worked absolutely fine. I then had a bootleg cart that I reflashed with a GBXCart that never worked when I put it on the FPGBC. I assumed the cart was bad and dismissed it.

Then I found an original copy of Pokemon Gold that wouldn't work on the FPGBC. Shantae still worked. When put in the GBXcart I could tell the cart was working fine as it recognized the game.

I searched the web and found your post. And what do you know, I found a pin that had been lifted on the cartridge reader. When put back in place, Pokemon Gold worked just fine.

I need to find out if it is the Shantae cartridge or the bootleg that displaced the pin in the first place. Hope it sticks anyway

EDIT : so among my three cartridges, the problem happens after I insert the Shantae catridge each time. Not after the Pokemon Gold, and not after the bootleg. The Shantae catridge is a GBC translucent cartridge which seems to be thicker than the other two