So there are two changes - The Altek Lamp Driver and LEDs.
I'd suggest replacing a few of the LEDS with standard 555 globes to isolate the issue. Sounds like it is the LEDs. They might not be suited to the game. Different quality and manufacturers of LEDs can create different results.
Good to meet you the other day pin frog, agree totally with niño here but try the non ghosting, no-flix option first as it may just cost you a little less than alter board
