Quoted from ChrisHibler:There is nothing wrong with the clock circuit. You can rule that out.
The reset circuit is suspect.
You can manually ground pin 40 briefly when the game fails to boot. If the game boots after that (every time) then the reset circuit becomes a strong suspect.
I almost always scrape the parts and use the DS1811 equivalent (noted in PinWiki). At the very least, it reduces quite a few parts down to a single component.
I had nearly the same problem with Mars: God of War a few months ago. It would only boot about half the time. I determined it was the reset circuit by grounding the reset circuit as described by Chris. Installing the DS1811 was easy and fixed the problem.