That seems REALLY odd, and maybe Trannyman might shed some light on this. But if the output shaft is coming with the axle, you would have to be breaking loose the snap ring in the differential and the passenger side axle and Im not seeing that happen without there being some other issue.
You have to use a wedge like a chisel to force the differential off the snap ring of the output shaft so if your out put shaft is coming with the axle on the drivers side, that would scare me a bit. But also keep in mind, on the drivers side, the axle is a female end whereas on the passenger side it is a male end on the axle.
Im sure you know this since you stated you had pulled a few sets, but I just wanted to point that out as well.