Sometimes it happens, if you house cools down too fast. Do you have your blowers CFM or something set to come up higher, I think I have mine at 30 or 35.
Ours happen when the sun comes out, it maintains the temp and the FR drops down to next to nothing, then it takes forever to heat back up when the sun goes down and the thermostat has to catch up....
I hit the FEED=10 and let it feed for 10 mins to heat up faster, then turn the blower up to about 50% and it helps bump the temps up when needed in a hurry.
Yes, talk to the guys at coaltrol.