keramos I would get such a circular pattern
I recommend doing a test flat without cooling the camera, after letting the camera rest for a few hours from the last time you cooled it.
If the "warm" flats do not exhibit a problem, you could be having icing problems (not the hockey kind :-) from too much moisture in the camera; in which case, it is time to replace the desiccants.
That being said, you can take flats with any reasonably bright source that does not require you to use long exposures. In which case, there is no need to cool the camera when taking flats, eh? The dark current noise increases linearly with exposure time; so there should be no reason to cool the sensor with 1 or 2 second type of exposure.
Chen