Awesome, thank you for all the replies!
I've checked the roms against ROMIDENT and they seem legit.
I've found the up/down count dip setting as well. It's currently set to count down, but the same scoring problem happens if it's set to count up. I've also verified all the other settings against the manual. One item of note is that there is no setting called out for number 8, but it doesn't seem to matter which position it is in on this particular game.
There is no acid damage.
I've checked all diodes and caps on the board in relation to the PIA lines.
I've also checked the matrix with all the dips set to zero and ruled out the playfield being the issue by using a jumper in the backbox.
Here's were it gets confusing...
When you hit number 5, it will decrease the score more than five points. If hit a second time the score will increase, again more than five points. Upon the third hit it will decrease again, but by yet a different amount.
If you reboot and start a new game, hit number 5, the point values will match what happened the prior game. This goes for any of the target values.
More wonkey-ness is that only about half of the switches match the "manual's" chart, the rest will often just be duplicates of these number, BUT... any target hit during a game will show correctly on the dart board. Also all the D A R T letters, X's, and saucers work correctly in game play as well. In other words everything switch-wise appears be being tracked correctly (regardless of the diagnostics miss-information).
I've compared the mods made to the board against the GP instructions and everything appears correct.
I am wondering if there might be a problem with the board strapping (jumpers) but the 2732 roms have GP labels on them (so I know they are original) and by all rights the board shouldn't boot if they weren't being read correctly.
The game basically appears to function correctly except for the scoring, there doesn't appear to be any problems with the controlled lamps, sound, or overall game function.
The only other thing to mention is that this was a Playboy (MPU17) but the board in the game is from a Centaur (MPU35) but I don't believe this would be a problem if strapped correctly. I'm open to hearing that I'm wrong here though...
I'm really at a big loss here...
Thanks again for the replies so far!
Still interested in anyone else that has one of these and can confirm how their scoring works. Also possibly if they have the same discrepancies in their diagnostics switch matrix test.