We just tested it over a course of ten rams, and the damage negating effect seems to be completely gone. Both ships sustained substantial damage from moonshine/kero/stamina head on rams. So, whatever it was that was causing the negated damage has gone away. I am not sure what could have been causing in in the first place, but the rams felt different this time. In the previously mentioned tests, both ships would slow down like they hit a wall of jello right before impact, would hit, and slowly bounce back with no damage and often not a secondary hit. This time, there was no slowing down, the ships would not bounce back much, and often there was a double or triple hit.
So, problem solved, somehow.