I have a similar problem.
My family and I have laughingly come to refer to it as 'Resting ****** Face'.
I can be totally Zenned out, at peace with the world, and apparently still look like I am actively seeking someone to murder.

I am currently working on smiling more, and making less eye contact. I am a very intense person by nature, and tend to make aggressive levels of eye contact without realizing it. I discovered both of these while taking an 'Interpersonal skills' course for work.

You might consider making a study of body language, your own and others.
Best of luck, I know how frustrating this kind of problem is.