I have what's I like to call "resting jerk face".  I've heard women call it "resting bitch face". I've had your exact situation before.

What I do is explain to them "resting jerk face" is just my natural relaxed face and then I assure them that I'm happy and that I can't really change how I look. I then say that I don't want to fake a smile because I don't fake well. I also say that what looks irritated to other people is just me thinking really hard.

The reality is that they will get used to it. Just be consistent and say that you can't help it help it and reassure them that you're a happy person.

I would relax though. You're not going to lose your job because your boss thinks you don't smile enough as a programmer.