Hard to say why your HDL isn't higher, but everone's adaptation of Primal differs, in what they eat and their activity level. But remember that your lipid panel numbers are a metric of probability, not certainty. In other words, if you are eating well and are in shape, I'd rather have low HDL than be out of shape and eat the Big Mac and Fruit Loop diet. Some people with admirable cholesterol readings will fall over dead, inexplicably. So while we may aim for higher HDL, it's not the be-all per se.
That said, if you are overweight, your HDL may improve as you lose. You don't mention whether you eat eggs, but that's one possible food source to raise HDL. I consume a good bit of extra virgin olive oil, and my HDL numbers are always solid. Make sure to eat magnesium-rich vegetables or to supplement magnesium - I'm not certain of the connection to HDL, but it does seem to be related somehow.
Beyond that, just stay the course and don't fret if your other markers of health are solid. If your BP, serum glucose, triglycerides, etc. all come into the target zone, HDL may not be such a big deal.