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@provenrad
I think the OPs saying that the wheel is either perfectly aligned between the chainstays (BB) or the seatstays (Saddle), but never both..?
I agreed with edmundane about checking the wheel first, both for dish and for a bent axle. is it a fixed wheel / singlespeed? single sided / Flip-Flop. Try putting it in the other way around and see how it lines up.. it could well be that it needs re-dishing.
if the wheel is fine then your rear dropouts are almost certainly misaligned / bent.. decent local bike shop can check & fix (if steel frame) this for you.. £s though.