How will calibrating the compass fix that?
The problem sounds to me like fluctuating power to the motors.
This could be caused but a number of reasons.1. Faulty esc.
2. Firmware failure.
3. Battery failure.
Certainly not by a compass error.
I recommend you upload a flight log with this fault happening so the gurus can have a look at it.
http://www.phantomhelp.com/logviewer/Upload/
Up load the log and paste a link to the log file here.
Hopefully someone with some experience in this will be able to give more definitive answers.
Looks like it could be a bad prop. Inspect carefully for any chip or ding in the blades. A small chip in a prop or two makes for jerky stability when hovering or flying.