The reason for this was discovered and we do offer a firmware upgrade to solve it. Please contact the shop (315-299-3589) to arrange for this, make sure to let them know it is to fix this issue. It is hard to avoid this time of year due to the stove running at idle a lot. In the winter it can be avoided by setting your CFT setting to something below your normal FR, which will leave the fan running at minimum most of the time and avoid the restarting issue. Happily, this issue does not cause any damage of the motor or anything, it is just annoying to some.
Thermostats with V3 002 through V3 074 version firmware are susceptible to this. This was fixed in V3 075 (V3 078 is the shipping code and what will be installed for the fix).