I am taken by the intermittent appearance of your problem -- some frames seem as much as two stops underexposed.
I very strongly agree with making some simple tests to see if the shutter is off.
The one thing I have not read in this thread is the issue of the M6 meter sensitivity pattern. I'm wondering if you are shooting with the M6 as though it had the Pentax metering pattern, and whether the different distribution of light and dark in your photo subjects may explain your problem.
If you google "M6 metering pattern" and again "K1000 metering pattern" you should get info that would allow you to decide whether your metering procedure needs adjustment. Good luck.