The datasheet says the I2C interface is fully licensed. I assumed that this means that it works, but I'm having my doubts.

Analog supply an example program, and driving the I2C peripheral is pretty simple. I've determined that the problem is with the write operations, not the read operations. After a 'bad write' I can power cycle and the data read is the data from the previous 'good' write. Basically the read data always gives a good result. The write operation doesn't use a repeated start, so I'm not focusing on that at the moment. The writes either happen or they don't, I never see corrupted data stored, so my suspicion now falls on the timing of the stop bit. I'll try and figure out how to trigger my scope on the stop bit.