Do you shoot these mags in the same order?
Ex; Load all three, then shoot them as marked (one, two, three).
If this is the case, your shooting technique while shooting the 3 mag group could be the issue, or you may have conditioned yourself to "know" you inserted the "bad mag" and get "slappy" with the trigger.
My suggestion, cover the mag numbers with tape (so you don't see the numbers, and therefore don't "know" when the bad mag is in) then load/shoot each mag individually, several times in succession. Does one still shoot low/left?
That's all I can think of.