Have you verified the waveforms with a scope? Are the rise times in spec?
so checking with an oszi, on GPIO2 or GPIO5 the level is about 0.75V which seems to be a HIGH actually. LOWs are really around 0.1V, and the shape of the signal looks not that bad, however, to me this seems to be super super low level for a HIGH...
I have removed the 12k resistor, so we are left with the 1k+3.3k, however, that did not change anything concerning the levels (and obviously that meant a change from 720 to 750 Ohm only)...
I wonder if we should take out the pull-up resistors in their entirety....