Scott,
It is not uncommon for the lens not to line up at 12:00 straight up. In fact, on my Bessa R, many lenses line up just to the left of 12:00 as I look down while holding the camera at chest level pointing away from me. If I were looking at the lens straight on, it would be lining up at about 1 or 2 o'clock. That sound right to you?
Now, with that said, it is more important that the focusing tab that sticks out of the back of the lens line up with the 'foot' on the camera that senses it - that informs the rangefinder where you have focussed your lens anyway. Some LTM lenses have a 'collar' that goes all the way around the lens, in which case this would be even less critical.
One thing to beware of - Braun Paxette and Super Paxette lenses are 39mm thread mount too, but have a different lens registration distance and won't focus correctly on a LTM camera no matter what. A clue you have one is when the focus readout is on the bottom of the camera at 6 o'clock instead of somewhere on top between 1 and 2 o'clock.
I have some lenses that line up just at 12, while others are more or less off - but they all focus correctly.
Best Regards,
Bill Mattocks