DMP only sends valid data to FIFO every other interrupt

I am using the DMP and sending accel and calibrated gyro to the FIFO @ 100Hz. I get an interrupt @ 100 Hz but when I read the FIFO contents register it only shows available bytes every other interrupt, so I am effectively only getting data @ 50Hz. If I was to read the FIFO count registers (0x72 +0x73)every time an interrupt occurs it would look like the following:
0
12
0
12
...

any ideas? Why would an interrupt be generated if there is nothing in the FIFO buffer? I am following the driver c code that was distributed around 18Jan13.