IMO it's not Av, but your metering mode is the culprit: Evaluative.
This mode "evaluate" the scene based on several areas
and certain round off in computations may result in a slight difference... especially if you let the camera chose its own AF point where the metering areas
around it may shift.
Try to switch to Partial or Centerweighted metering and the results will be more consistent...
:idea: -> BTW you can also put the camera in manual: The camera will automatically switch to Centerweighted metering and you can fix both
the shutter and
aperture with flash.