OK, it seems I found the reason for varying measurements.
Temperature swings. When I’m not home heating doesn’t work and temperature goes down by a couple of degrees. I didn’t expect this would be a problem as the cells being measured would be very warm after I return despite quite low ambient temps.
But I took the charger to my fiancee, she measured the 18650B 3 times within 30 mAh. Above 3500 mAh. So I can disregard all the measurements I did so far, but it doesn’t mean there’s a problem with the charger.

The resistance variability is not temperature dependent though…