It's a reasonably new ( <2 years ) monitor which hasn't seen a ton of use. While I've known EL caps to go bad in that kind of timeframe, an inspection of the monitor chassis doesn't reveal any with telltale signs. The signal from MK2 seems identical to NBA Jam TE in terms of what I can measure - all frequencies are the same to within 10Hz on the horitonzal, and 1Hz on the vertical. I have not examined active video timings relative to synchronization between the two, but geometry is the same, suggesting that the active video areas are likely the same, as well. The cabling is exactly the same (I'm just swapping the JAMMA harness over). I've also completely redone the video harness in response to this problem with no luck. The fact that NBA Jam TE runs fine on identical hardware with (near as I can tell) identical timings says to me that it's not just some issue with it not liking the mode MK2 runs in.
As far as compatibility, everything is within the specifications published by Kortek. As to the monitor actually performing to spec, who knows. Of course, being a digital monitor, it may not be quite so tolerant of drifts during operation, which could be what's happening. Everything always starts out fine, but generally within 5 minutes this problem crops up.
I can try running it on another cabinet, though I don't have access to any other generic JAMMA cabs - the closest I can get is a Dance Dance Revolution cabinet, which is at least JAMMA for some things, including video.