It's possible this is a hardware problem, but what I'm seeing is this...
The clock is enabled on pin 0, data on pin 4. With both enabled in exactly the same way, drive mode S0D1, and with an internal pullup, the clock pin works as intended, but the data pin is pulled low. This happens even with no other devices on the TWI lines, only a logic analyzer.
I can set the data pin to S0H1 and it goes high; if I set it to D0S1 it also goes high, but seems to change state at random when the clock pin is toggling in the twi_master_clear_bus() function.
I'm wondering if it's the same problem as this, or whether that's only a problem for the BTLE soft device?
Any other ideas?
