This baffled me for a long time but ended up being really simple.
When the player died and the Continue countdown came up, it would only count down to 7 then returned to the title screen. Logic suggests that this shouldnt be the case and checking in MAME proved it.
The problem ended up being button 1 for player 2 was stuck on.
Traced the stuck low signal through resistor array CRA3 and to a 74LS253 IC @ D19. Pulled and replaced the IC now all is happy.
I wired up the non jamma board I recently got, its a SEGA board marked up as Pitfall II but at some point the ROMs had been swapped out for Wonderboy ones. I already have a Wonderboy board and prefer them to be original so I burned a new set of Pitfall unencrypted roms and swapped them over.
I noticed the the game also had a fault where the left side of the screen was repeated on the right side. After a little tracing out I found a 74LS283 with a floating pin, I swapped this for a spare and fault fixed.
Not a fan of this game, will probably sell it.