The problem was the video output had black bars going through it, a google search brings up two or three other people with this problem but not much else.
I was convinced before it arrived it was going to be a overheated GPU problem but once it arrived this was quickly ruled out after plugging the gamecube board directly into the TV and it having no image problem. That's right these Triforce boards use a standard japanese gamecube motherboard, the only difference is the IPL (BIOS).
This is what the image looked like both in 15k and 31k mode.
Next I wired up Red, Green and Blue from the input pins of the Sony CXA2067AS (video amplifier) on the bottom PCB directly to the monitor and taking sync from the vga socket (sync doesn't go through the amp).
No more black bars, so the amp is bad right?
I also isolated the three output pins from the board to confirm nothing after the amp was causing the problem and it wasn't. So I ordered a replacement CXA2067AS from China, after waiting a couple of weeks for the replacement it ended up making no difference, and the black bars remained. It's possible the chip from China was bad as these are now obsolete it could be a pulled / used and untested chip but I am not so sure.
Either way I wasn't going to wait another two weeks for a replacement and decided to use what I had on hand. I bypassed the original Sony amp and used a TMS7314 amp which I already had from previous N64 rgb mods that you can find here.
Not pretty but it did the job.
Ready for some Mario Kart GP goodness. :)
Although 'fixed' I didn't quite get to the bottom of the exact cause with this one. If it wasn't a bad amp I believe it has something to do with settings stored on it, but this isn't confirmed.