Sounds like a memory protect issue. The memory protect line prevents data being written to the 5101 (battery backed RAM) or NVRAM unless
a) The driver board reports everything is A-OK, OR
b) The coin door is open

So in your testing, you satisfied condition b, and it lets you add credits. But then when you close the coin door, if condition A is not satisfied (for whatever reason), the MPU will prevent any writes to the 5101/NVRAM (though it still keeps track of your credits in RAM until you cycle power).

BUT, that's Sys6 behavior. I believe Sys7 got rid of condition b. Are you running a Sys6 MPU board by chance?
(edit: No, of course you're not, as Jungle Lord won't run on Sys6)

OK, here's the Sys7 behavior: With the coin door closed, the memory protect is supposed to prevent writes to the SETTINGS area of the 5101...settings that control things like credits per coin, etc. But it should still allow writes to all other locations.
I'd guess that when the coin door is closed, your MPU is preventing writes to ALL of the 5101 (Or it is at least preventing writes to more than just the settings).
Does everything work as expected so long as the coin door is open?

IC12, pin6, on the MPU gates the R/W line to the 5101. With the coin door closed, this pin should be toggling, as it is essentially the A7 line.