You can be at the wrong med level or on the wrong med for you. I have tried almost all US thyroid med, finding the correct dose is tricky especially if you have Hashimoto as opposed to just under active thyroid.
There is a lot more to Proper thyroid treatment than the average doctor who looks at TSH only and prescribes only T4 meds. You really need to know where you feel good in the Free T3 and free T4 range, TSH is not so important. Most MD's are backwards on this thinking - poor training.
I suggest posting on the thyroid disorders forum here at Medhelp , not fitness.
U can take your thyroid med at anytime n the day, u just gotta make sure it at least 2 hrs after u eat or B4 u eat at all. Just as long as u have an empty belly. The hot flashes may b cause by the gland getting a "boost" from yhe meds. I kno that ur meds help with energy levels so your body's prob gearing up! Then again if ur havin this much of an issue u might be on a wrong dose. Ur levels should b checked REGULARLY. Most peoples levels never stay at one number all the time.