The whole point of having the origin texture is for defining origins. If it were a matter of order you could just use nodraw. But you can't, because that's what origin is there for. I would very much like to get a step-by-step reproduction or a video for the problem you're having...
The only problem related to selection I'm aware of is with copying - if you clone an entity, pressing N will edit the original's properties, not those of the selected copy.
Anyway, as for wobblyness, that may be due to patches being hard to make perfectly round due to math.