I got it working.
I edited the file in the twiddler tuner, and changed one chord with a rather long output which I didn't need to a shorter one. Then I saved and downloaded the new file, swapping it with my existing config.
My guess is that either that chord was too long somehow, or the cfg validated in the tuner but didn't actually work on the device, and the new cfg was output in a more friendly format.
Either way it's all good now, so you can either close this or leave it around to potentially help others with the same problem in the future.