Guess #2: there are small accelerations due to the device's interior magnetic field trying to align itself with the earth's. This won't really go away in space at any plausible orbit. Although they try to mitigate magnetic fields due to the wiring, they don't seem to test for the internal magnetic field geometry vs the earth's magnetic field.
Interesting hypothesis. Yet how would this work for ultrahigh frequency, aka microwave, aka AC fields? (Or does a magnetron act like a rectifier to create some DC components in the waveguide & chamber?)
I suspect a time dependent mass gap possibly could explain why the EmDrive could indeed workTime Dependent Mass Gap Implications: The Possibility of the EmDrive?
(I added a section 7: EMDrive speculation in relation to a time dependent mass gap). Under atomism the mass-gap must be time dependent, while all masses larger than the mass gap seems to not be time dependent relative to each other. The EmDrive can be seen as a series of clocks with different frequency laying side by side, with a time dependent mass-gap this could likely give some thrust. Well yes quite outside standard physics.