I have dual sided Garmin Vector pedals on my Trek and on my indoor bike (Lemond Revmaster Spinner-type bike). I have noticed that on my road bike a L-R balance of 52%-48% would be typical. On my spinner bike (set up just like the road bike as best as I could) a typical L-R balance would be 48-52. It could be that one of my pedals is out of calibration but it is also possible that subtle changes in setup between bikes can change your L-R balance (I don't know this but it seems possible) and since you are only reading one pedal, that could possibly be one source of the power difference that you are seeing.
dave