I have a fork with minimal changes, and am using the same QMK software and have discovered an issue with pressing multiple modifiers.
It turns out that the order I press the modifiers is important. If I press say Shift on the left half and then some other mod on the right half and then the actual key, everything is working as expected.
But if I press the modifiers in the reverse order, it doesn't work.
Is this something you have experienced? Is this a QMK issue?