I've had plenty of I2C headaches but that's not a glitch I've seen before. Are you using the SDK's I2C API? Sure you're not touching any registers that might affect it? I agree with Mark that it's most likely a firmware problem. I've never used it with a level shifter, though. I was going to suggest checking that something in the hardware isn't pulling the line low but it looks like the high interval in the runt clock is dropped almost completely, and if something else was pulling it low the position of the other clock pulses would be unaffected, so it has to be internal to the part.
Maybe set a watchpoint on I2Cx_F and make sure nothing is messing with the frequency divider?
Scott