My observations are consistent with your impression and don't think we should try to do anything about it.
I also suspect that an analysis of tone -- roughly speaking, to how obnoxiously the commenter comes across -- would account for a large chunk of the variance.
I was just trying to think of what obnoxious means in this context because, well, who of us wants to come across as obnoxious? And I think it means, with some latitude, that the writer suggests that he or she is aiming at something different than what the other participants are aiming at. This could be egotism/narcissism, persuading others towards a pet belief system, or taunting others/trollishness.
The other alternative could be issues concerning rhetorical style. Either the rhetoric of the writer is uncomfortable to what the reader is accustomed to, or the emphasis of the posts makes it difficult for readers to pierce the arguments for substance.
Or other meanings I'm not aware of.
My impression is that critiques of lesswrong mainstream positions and arguments for contrary positions are received well and achieve high karma scores when they are of very high quality. Similarly posts and comments that take lesswrong mainstream positions will still be voted down if they are of very low quality. But in between there seems to be a gulf: Moderately low quality mainstream comments will stay at 0 to -1 karma while contra-mainstream comments of (apparently) similar quality score solidly negative karma, moderately high quality mainstream comments achieve good positive karma while similar quality contra-mainstream comments stay at 0 to 2.
Do you share my impression? And if this is the case, should we try to do something about it?