For the multi slots it is best to use the multi carts that do not have the external daughter board. Past that the biggest thing I've seen with the multi carts is to only use them in the system(don't put any standard carts in as well) and if problems come up it is generally voltage on the 5v line. That and just crap hand soldering on the multi carts. I've had to fix some bad solder points on a few in the past.
Also with a bunch of the multi carts just an fyi check the soft dip switches when you go into a new game. On a few of the carts some of the games have weird settings or are set on 8(hardest setting) by default. The cart saves the soft dip settings so you should only have to fix them once.
Also you want to clear the memory on the neo geo motherboard. You do it by going into the test menu and hit a b and c when prompted. Had to do it twice on mine. I also had some issues with mine(2 slot golden) and the 161 cart when I had the neo geo memory card installed.
Yea I've also read of some issues hooking the ones with the daughter board into some of the multi slot boards just because the cable is short. Just a real tight fit.
Another thing worth mentioning from my experience. On the 161 cart I have it says hold player 1 start for 5 seconds to go back to the main menu. Seems to take a good bit longer.