Hi Alex,
I stumbled across this thread due to having similar problems with the LSM303 module from adafruit.
With the LSM303 we were having no problems using it with the Arduino boards, but once we moved it to the NP2 we started to see the issues and couldn't communicate with the device (bytes transferred was always 0). We attached it to the scope and saw nothing on the SCL or SDA lines (just nice 5V or 3.3V lines). However, we noticed if you start the netduino and I2C communications and then you remove the SDA line and then reattach it communications starts up and continues without a problem. Also, software I2C class worked without a problem (although it is much slower) -> http://forums.netdui...und-for-plus-2/
I don't believe the problem lies within the LSM303 module as it works with the arduino and the software I2C class on the netduino.
Chris,
If you do plan on trying to debug this please let me know and I will get you any information you need. It looks to be on the Netduino side but I don't have any other I2C devices or netduinos to test with so I can't determine if this is possibly just a faulty NP2 or an actual bug.
(For reference I am running the NP2 with 4.3 under VS2012)