Stuff like this is frustrating isn't it!
Have you run my RAM and CMOS tests on it? Perhaps one of the memory addresses doesn't hold a value properly. Those tests check the entire address ranges of each chip. Running the RAM tests is essential too, since the Williams ROMS may simply copy the value in the 5101 to an address in RAM and never look at the 5101 again..
You could also run the edit_cmos ROM and browse through the actual values in the 5101 chip. Since the chip is 4 bits, an 8 bit number is stored in two consecutive addresses. So for example, the GREEN ROMs expect the Number of Balls per game to be stored in the 5101 at absolute addresses 419=0 and 420=5 (in this case 05 balls per game). As you've already noted, YELLOW ROMs have slightly different absolute addresses, as do the other colors of system ROMS.
When you boot the edit_cmos ROM, Player 1 display shows the absolute address in decimal, and player 4 display shows the value in that address (also in decimal).
The addresses before and after 419+420 are used for the related functions in the game setup (High score to date, Replay 1 score, Replay 2 score, etc). I haven't mapped out all of the addresses, but with the editor you can at least browse the values and change them beyond what the Williams ROM will let you.
Mabye that helps you, maybe not, but you can at least use it to examine the contents of the 5101 and maybe make some sense out of it.
For those who don't know where to get these test ROMS, they are located here: http://pincoder.reversion.ca