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jt_cph_dk
There may be a misunderstanding. I do own a m42 lens which will not fit in any of my Pentax bodies if I fix the adapter on the lens first. With this lens, I found out the reason is that the adapter is screwing to far onto the lens; when I try to put the lens/adapter combination onto the body, the adapter is not moving far enough into the body (it is just a fraction of a millimeter), so the bayonet will not turn. This happens with every adapter, also with original Asahi Pentax ones.
With this lens, a shim of about 0.3mm between lens and adapter fixed the problem, and I can still focus to infinity. As you were not sure about the reason for your problem, I just thought it would be worth a try. If you face the same problem with a lens, and a shim is curing it, this will certainly not fix an existing infinity problem, as you are widening the register distance, not shorting it.
Added:
About the "not aligning": I sold all my m42 lenses but one, however, I remember none of them did align perfectly. I don't feel this was a disandvantage (specially when the misalignment was -10 to -15 deg.), because of the overhang of the built-in flash of modern DSLRs, which hides the scales of the lens, if it is at 0 deg.