Which menu are you using? The original one with blue background / white text, or
the updated one?
I'm just wondering what the reason for it not working on the PBC might be. The PBC has no BIOS that I know of, so it shouldn't be a checksum failure.
There are some subtle differences when it comes to the VDP, but the updated menu doesn't do anything that isn't supported by the Genesis VDP (AFAIK, since I don't have a PBC). I can't say for sure about the original menu.
Another potential difference could be the amount of power supplied to the cart when using a Master System VS a PBC.