weird isn't the word!!!!!!
it is theoretically possible that the wheels out of line might, and I must say its a very speculative "might", cause an accumulated error in the sensor memory.
its really doubtful but you have eliminated almost everything else.
as a matter of course, if the wheel alignment is out, I'd get the tracking done.... preferably on a 4 wheel rig (most newer laser units are 4 wheel) preferably by someone who uses a spreader bar (merc settings are all with a spreader used) if not a spreader it won't matter too much.
its a good idea for stability (especially in winter) and to reduce tyre wear...... who knows.. it might actually change things.