Primary Investigator gets really nervous around me?
I would advise you to simply ask about it, in a way that pre-supposes as little as possible.  For example, you might say something like:


  Can I ask you about something I am feeling concerned about?  I've feel like our interactions become very awkward and stumbling sometimes.  When I see you talking with other people, however, I do not see this happening.  I'm concerned about this, because I want to have a good advisor/advisee relationship and be able to communicate effectively with you.


Don't assume anything about her feelings---what you might be interpreting as feeling nervous might be something else entirely, even just a mannerism of your PI.  You also may be incorrect that this is unusual with you: people have strong observational biases and also you don't see your PI when she's alone with other people.

Hopefully, the two of you can then have a short awkward conversation that will help resolve (or at least allow you to work effectively despite) your other awkwardness.