I use nvram in all my Williams games, Robotron, Joust, Defender, and soon a Stargate I'm restoring. They work great but i find it's important to have your 5v set right especially if you have a switching power supply. If your 5v is too high then it's possible it's write protect won't trigger in time to prevent corruption of the CMOS data during shutdown. If it's too low then you could have weirdness even during gameplay.
From what I recall, on Defender if a high score got corrupted you would still see it in the high score table but with weird characters, like a ? symbol as part of the score for example. I noticed they fixed that with later games like Robotron (and presumably Stargate) where the game will do a verify on the high scores and remove corrupt entries. So if you suddenly see a high score entry dissapear it's because it got corrupted somehow and the game caught it and removed it.
I mention voltage because I find Williams games are weird because it seems like they can work fine even as low as 4.6v but that may cause weirdness with the nvram. If you measure your 5v at one of the RAM chips, what reading do you get? It's just a guess but maybe your 5v is off a little. This type of error won't get caught in any of the tests because the machine works fine at low voltage , but it makes the nvram get finicky.