Sorry for the very late reply on this and probably anything else. I’ve missed over the last half a year again… Anyway, you’re right on the money on this. Back in the day we used to have advice that anytime you switched a game you should boot the system without a dongle in it and power cycle it a couple times to “clear “what was currently being loaded.
Now that said, what I believe is actually happening behind the scenes is that each game has a different load for the Namco board side FPGA, and because that FPGA is responsible for everything from jam/JVS to IDE operation, mismatches between the version that’s loaded and the game that you’re trying to load will cause the game not to load. Now I’m not sure what the criteria for clearing the FPGA and reflating, but my suspicion is that some games actually either check the version first or simply just flash it anyway on boot, while others, if they find any FPGA code simply just use whatever they find because it sort of seems to work.
Just my observationally based assessment of the situation, I don’t have the technical know how to actually debug the system and see if this is actually what’s going on.