Perhaps since cutting out the nut flour/paleo baking you have gone too low carb for you body to handle? Perhaps try adding in a few primal carbs - sweet potato, fruit, honey?
ETA - I am actually struggling with the same issue right now. I lost 50 lbs with no problem and just gained back 8-10 lbs. Not fun. I hope I have tracked mine down to sugar, but I am still feeling a bit tubby.
Using low lectin/nightshade free primal to control autoimmune arthritis. (And lost 50 lbs along the way )