Unfortunately, the LED board wasn't the issue either. I pulled all the piggyback connectors and reconnected the originals. No difference.
I'm way out of my depth to try and figure this out any further on my own. Of course, it's not a big deal at all and I'm fully prepared to just live with it as a minor quirk of my machine. My only trepidation is that it could be indicative of something that could have an adverse affect down the line. I doubt it though, as it's been like this for years and otherwise, the game runs flawlessly.
That said, I'm always open to suggestions.