I don't have an oscilloscope but if it's necessary I can get one, it's been on my list to buy one for a while.
The reason I don't think it's a Kiwisix problem is because I had the same exact problem prior to the Kiwisix mod. The only reason I actually bought the Kiwisix is because these the same buttons didn't work when I repaired the KLM-367A and I thought it was a battery corrosion issue with that board.
But you're saying all the logic should be within the 8049 chip, not any of the IC's near it? I'll check to make sure all the pins from the 366 processor are connected properly.