I assume that none of the keys from layer2 are working? I would guess you have your layer switching set up wrong, but I can't determine that with certainty until I try it (which sadly won't happen until I solder my switches down)
I'll have to check, but I think the "layer toggle" is momentary, which possibly conflickts with the 0 (ins) also on that key. If I'm right, then layer push/pop would be non-momentary. Again, I'll have to check.
Bytheway, that's an excellent layout. I especially like the reversed right hand on layer3
Until I can get a working board to check your layout with, you'll have to wait for someone else to help you.