A couple things I can think of -- if your thyroid's been wanting iodine and now it has it, it might be trying to ramp up production but sort of creaking along in the process. Another thing, during your break from iodine, bromine or some other toxic substance got a foothold in the thyroid's iodine receptors, and iodine is trying to kick it out. The old standbys of salt-water flushing and increasing your dose come to mind. I liked Spudlydoo's take on this:
when I first started Iodine and companions I had a very sore throat and thyroid for about 2 days, couldn't swallow without a lot of pain. I decided to up my dose of Lugols to 16 drops 2 times a day and the sore throat and thyroid were gone within 24 hours. The same thing happened to my friend when she started, she had a large thyroid nodule on one side, she increased her dose (along with increased doses of the companions) and her nodule and pain dissappeared within a couple of days.
I also had an extremely runny nose at the same time as all the pain, but increasing the dose took care of that as well.
Everyone is different, some people like me, when experiencing detox symptoms will use the sledgehammer approach, some like to pulse or stop altogether until symtoms stop. It just depends on the individual.