Mine used to do it a lot whether out hacking or during a lesson and sometimes it was so bad she would hit me in the face. I used to think it was a sign of discomfort and I'd be constantly asking my instructor about her bit, her saddle, her back etc etc.
However over time I've come to realise it was a sign of tension/stress and now we are a much more relaxed partnership she hardly does it at all. The odd time she does do it it's because something has worried her or I'm asking her to do something she doesn't want to do.
Is it possible she is a bit nervous hacking on her own or are you a bit tense being out on your own?
Mine does it out of nappiness/stress. I had his back checked and was sore and his saddle didn't fit when I bought him. I sorted out these problems and he relaxed a bit but still did it when I pushed him to do something he found difficult when we were schooling or when he didn't want to do past something out hacking. I try to deepen my seat, keep loose contact and be persistent and encouraging with lots of praise. He is getting better, he was very stiff on one side and did far more head tossing when were schooling on that rein.