Sorry for the delay in replying, we're just getting back from MASTERs in Phoenix ourselves.
Can you verify which profile you OTAed to your Modulo-2? In the profile folder in the example project, there's an afBlink profile and an afBlink2 - the first one is for the Modulo-1 developer board (an older model) and the afBlink2 profile is the one for the Modulo-2 board you have. Unfortunately, profiles between the two device types are similar, but incompatible.
It does look like the board is communicating properly, the mcuISR debug statements are printed when the MCU receives an interrupt from the Modulo-2 board (indicating the Modulo-2 has data to present to the MCU).
Can you verify that the Modulo and it's Xplained adapter board are plugged into the EXT1 connector on the D21 board? I don't think it should make a difference but experimenting with it a few times it actually seems to make a difference to me.