For example, the amount of time the ghosts are blue in the Pear level and the Banana level is not correct. It's like their timing is switched.
I'm not really an expert about Ms. Pacman (the actual arcade), but I was toying around with the emulator in Mame. Under the cheats menu, there are the following options, which affect the length of time the ghosts are blue:
--Practice Speeds--
-stay blue until eaten
-slow changeback
-moderate changeback
-quick changeback
-lightning changeback
-no change to blue
I was thinking... in order to create these cheats originally in the emulator, the cheats had to be discovered by exploits in the rom(s) correct? In other words, to enable the cheat it inserts code into the original rom to alter it's behavior. As such, would it be possible that the CPU that you had repaired is flawed? It may appear to be working correctly for certain levels, but when you get to other levels in the rom the data is somehow corrupt and the ghosts are behaving abnormally.
Again, I'm not an expert, but at least it's something to consider.
- DeLuSioNaL