Some frame need an offset rear wheel, I've never seen an offset front wheel however...
It's not in a frame, but a jig which is set at central positioning (I guess a self dishing one.)
To be honest the spacers shouldn't matter but just something to check as it should still be central when flipped.
All I can think of is the hub is to loose and not being clamped tight enough like it would in a frame so it's got a bit of slop, but you would notice that by rocking it.
OR it's just clamping slightly wrongly in the stand. But you don't have big axles, just standard 9mm ones.
Or you've been drinking a bit to much.
Dish it up the way you want it in the front forks, it should then be 'correct' that way around.