I have been on thyroid meds at least 20 years with occasional night sweats. In the last five years they have been increasing and I was dx with T-cell LGL Leukemia Nov. 2007. Now they say I am Menapausal. Night sweats occur with all three. The thyroid regulates hormone and we have been lowering my thyroid meds lately. The more I regulate all three the fewer sweats I have. I also have a friend, recently dx with both low thyroid and pre menapause, she has had trouble with body temps. It should get better once your meds are regulated and hormone levels get back to normal. Supposedly, there is a difference between synthetic and organic thyroid meds, if it continues, I would try a switch. It is amazing the all the things the are affected by the thyroid. Hope it gets easier for you.
TJ