If I recall, the Nintendo PPU is a custom RICOH microcontroller. With the exception of a very small amount of internal DRAM, there is no EEPROM that I'm aware of. RAM and ROM data were handled by the game system and game.
If your PPU is showing the wrong colors for the game, you ight have the wrong PPU in there. Nintendo made more than one model PPU and many NES modders are scavenging the arcade PPU's for their RGB capabilities (---smurfing--- ---uvulas---). So if you swapped the games or the PPU got swapped, that might happen.
I don't know too much about the PPU's from a hardware perspective. Most of the information out there is specific from a software standpoint. I found a reference list showing which arcade used which PPU version:
http://www.johnsarcade.com/nintendo_vs_ppu_info.php. That might help you zero in on the problem.
If you still think you have a bad PPU, it should just be as simple as swapping PPU's.