I've got a real head scratcher. I've dealt with games not booting before, but my Space Shuttle has developed a unique booting issue. The game will not boot from a cold start and takes anywhere from to 2 to 3 minutes before it warms up and fully boots. During this time the CPU display indicator will say 7, but after warming up it will flip over to 0. I'll occasionally see some random lamp strobing and coils pulsing before it finally boots. After that, the game works fine with no issue or resets.

Here's everything I've tried so far:
1) I changed the power supply to a new Rottendog board from another machine. No change.
2) I installed an inkochnito board which replaces the big blue cap and bridge rectifiers. No change.
3) I swapped CPUs with my Comet. The issue is gone, so I know it's on the CPU.
4) On my original CPU, I changed the three 100uf caps and the 22uf cap in the power section of the CPU by the battery pack. No change.
5) I reflowed this entire section as well as all of the connector headers. Still the issue remains.

I suspected that the connectors might the next thing to change, but again it works fine with my Comet's CPU installed, so I don't think that would make a difference. Does anyone have any idea what to try next?

Someone on facebook said the U21 Crystal is most likely the culprit. I'm going to replace it and report back.