Otherwise, I'm at a loss to explain why this would happen. I've used MSR Whisperlites and similar stoves in all sorts of cold-weather conditions, down to minus 20 degrees Fahrenheit. Temperatures in the single digits are easily within the range of the stove's capability. Whisperlites, in fact, are renowned for being extremely reliable in the coldfar more than canister-fuel stoves that tend to freeze up.
So, I'm inclined to say you need to run a thorough test of the stove at home, and clean it as well, paying particular attention to the fuel line. To do that, remove the fuel line from the stove by unscrewing the priming cup, then pushing down on the generator tube to remove it from the mixer tube. Use a jet-cleaning wire to thoroughly clean the jet. Then remove the cable from the fuel line, wipe it off, and stick it back into the line, running it up and down to scour the inside of the line. Spend a minute or two at this, running it in and out at least ten times. Pull the cable out and wipe it off, then repeat the procedure. Re-insert the cable into the fuel line. Connect the fuel line to the pump and bottle, pressurize the bottle, and open the control valve to allow about a quarter of a cup of fuel to flush any debris out of the fuel line. Discard that, then prime it again, start the thing up, and see how it works.
And, be sure your fuel is fresh and clean. Water can form inside a fuel can or tank pretty easily.