Got in Gohan's system in today and think I found the issue. I'm pretty sure the NBM probably dislodged one of the pins on the 68k cpu. When looking closely at his system, the 68k was soldered down slightly askew. This could have led to a weak connection on the pins and when placing the NBM on top, it slightly dislodged one.
So far its the only occurrence, that I have seen, of this happening. The socket is a tight fit, so if the cpu has a weak solder connection, it could pop off a pin. So far no MVS installs have had this problem.
The 4-2 system I used to develop it never had a problem, and that was after popping it on and off at least 100 times. The 5-1 system of Murray's was the same, popped it on with no issues. CDZ as well.
The other problem I saw on this system was that the ribbon cable was peeling and not making contact from the MB. This seems to be a big problem with these cables. I trimmed his just above where the peeling stopped and it works fine.
As far as the CPU. I just went around it with my soldering iron re-melting the solder that was already on there. After that, worked just fine.
The CD systems seem to be a bit more delicate than the MVS, but I guess that's to be expected. They may need a bit more care with installing and from now on, I'll use a "softer" socket for these. It wont be as tight of a grip, but it will be enough to hold it on there. I installed a softer one on Gohan's and its been playing '99 Demo Mode for about 2 hours now, with snkdan's current bios.