My hot water heating system lights the burner when the water temp reaches the low limit whether the circulation pump is running or not. Is this typical of older systems or should the burner only light when the circulation pump is running?

Had a new home built in 2012. It's a ranch with a full basement. We went with hydronic radiant heat (fueled by a propane boiler) using the "warmboard" product for the main floor. This is the product where the pex tubing is fitting into grooves in the subfloor itself. For anyone not familiar with the product, It's supposed to be a more efficient method of heating as the heat is closer to the surface and allows a lower water temp to run through it and still effectively heat the home. Upstairs (2000 sq ft) has 4 zones, basement has a single zone. For basement the tubes are in the concrete. Anyways, first 2 winters, everything was fine. Very even heat throughout entire house. However, now, on colder days, the upstairs master bath is significantly colder (5-7 degrees) than the master bedroom. They are off the same zone. I can stand in the bedroom where its 70 degrees, walk a few feet into the bathroom, and its around 64 degrees. The tile floor in there will be very cold, kind of the opposite effect I was hoping for when I chose a radiant solution. And not sure if its related or not, but the basement space (which was made into an office space) directly below the upstairs master bath, is equally colder than the rest of the basement. The downstairs is on a single zone. If I close the basement office door overnight and walk in there in the morning, its quite cold. If I leave the door open, its not as cold as when its left closed, but its still not as warm as the rest of the basement. The space below the upstairs bath is the only part of the basement that is the least bit cold. I don't understand why I would have a cold spot in either sections as I would think if there was a problem with the water flowing through the loop then I would feel it throughout the whole loop. And just to rule out a couple of things, the windows are the same in every room, and the house is very well insulated. I spent extra above and beyond on making it a very well insulated home. Everything was fine the first couple of winters. Any ideas?