Well I don't mean to be an idiot, but I guessing you mean the Back-up Clear function where you hold A+B+C together?
I did that tonight and it actually did sort of help a little. The game will now play, however it wants to reboot the MVS an additional time before loading the game. And then it reboots the MVS again after exit?
Yes sir, that is what I am talking about, where it asks you to hit A-B- and C together in the main settings menu on the MVS cab, this clears something like the backup ram which, for myself, REALLY fixes many things. I used to have issues playing Neo Bomberman because the sprites of the characters would not appear, and the games for the NGDevTeam games would not boot in any other slot other than slot one, and would not game cycle if certain games were not in slot one etc.. executing this memory clear function fixed everything for me, and I seem to need to do this from time to time depending on the game I play, and the error I encounter. I also bought Neo Turf Masters from someone and though it was defective, because the score screen had garbled graphics, and when I went to hit the ball when playing the game, it would say time over within one second every time. Clearing the memory using the method above fixed that as well.
I can now even put EVERY GAME from the NGDevTeam in every slot, filling all 6 slots, and play all of them and cycle through them without an issue as long as I clear the ram/memory after inserting them.
(Yes I know you cleaned it already...but...) I am not sure why it is asking to reboot the MVS system each time before playing it, and after, but, what I can recommend is that you take the game out, open it up, clean the board contacts vigorously with a nice new soft Pink Pearl eraser, and make sure it is like new, and then use 90%+ IsoPropyl Rubbing alcohol on a soft cloth, and scrub the contacts on your game until the carts contacts shine like new. You might even want to do this to your cart slots on the mvs using a new tooth brush, and softly clean all the teeth on the MVS cart slots using that same IsoPropyl Alcohol, and make the slots shine like new. Then take your game and insert it in the slot you wish to play it in, and take it out. Put it in and take it out a few times, as this seems the kind of grind it down a bit, and get the contacts to really make contact. Then once all this is done, reset the ram on the MVS again a few times, and then turn OFF the MVS cab. Switch it on, and the problem SHOULD be solved. If not you might have some kind of faulty MVS board. Doing all of this might sound a bit much, but it has solved ALL my issues with ANY games I had problems with on my 6 slot board.
I hope that this helps you out. If not, James can help you further as he is the MAN that knows ALL about the MVS. Good luck, bro!