Being that this seems to be an intermittent thing, I'd guess that it's a saddle/clothing/position issue.

I'd take it back to the shop you bought it from and see if they can adjust the saddle to better suit your position. Generally, adjustments like these are free on new bikes so shouldn't be any cost to you. Just let them know what's happening and they can work with you. One of the advantages of buying a new bike from the LBS. Take advantage of it.