Well the NI7055 was sometimes used from the factory in place of the ER2055, which was the more common EAROM, I believe that my Millipede also has a NI7055 in it.
If your voltages all check out, and you have tried resetting your high scores after you replaced the 555, the next thing I would do is like John suggested and replace the NVRAM/EAROM chip.
For that you have a couple of choices, you can replace the EAROM with a direct replacement,Mike's Arcade has those
http://www.mikesarcade.com/cgi-bin/store.pl (just look up earom), or you can order one of JROK's adapter with a more modern EEPROM
http://www.jrok.com/hardware/earom/ . If it were me I would probably go with the JROK board because it's about the same price, doesn't need the odd voltages and is probably more reliable.