I run into the same issue once in a while and I'm pretty sure it's a voltage issue. When my batteries are fully topped off, the heat is amazing. If my batteries are a little low, (cold batteries tend to read extra low) the heat wont cycle back on.
Interestingly, it will turn on for a cycle if I manually turn it off and back on.
2005 Ford E-350 Diesel Sportsmobile
EB 102 Voyager top, 3.55 rear, Mobil 1 all around
270 amp alternator, billet water pump, coolant filter kit,
aluminum radiator, X-Monitor with pyro, trans temp, boost
+ Scan Gauge & SCT Live Wire (Economy)