It could very well be you have an allergy to the dye in question. You could do well possibly by switching to another LT4 which doesn't use dyes. It'd be cheaper. Or you could go with the 2 50's...
Since Synthroid has the rainbow colors to them, it's often the case that many people have a problem with allergies to the dyes - usually the Yellow ones. You are not the first case I've come across in my travels on message forums.
You should note this well and avoid any kind of other drugs or foods that have these dyes in them. Have you ever been on the 88 and if so did you have problems there? I'm trying to think of a way to figure out for you which of the two yellow dyes you have a problem with...
The List of Dyes Used in Synthroid
25 FD&C Yellow No. 6 Aluminum Lake
75 FD&C Red No. 40, FD&C Blue No. 2
88 FD&C Blue No. 1, FD&C Yellow No. 6, D&C Yellow No. 10
100 D&C Yellow No. 10, FD&C Yellow No. 6
112 D&C Red No. 27, D&C Red No. 30
125 FD&C Yellow No.6, FD&C Red No. 40, FD&C Blue No. 1
137 FD&C Blue No.1
150 FD&C Blue No.2
175 FD&C Blue No.1 D&C Red No. 27, D&C Red No. 30
200 FD&C Red No. 40
300 D&C Yellow No. 10, FD&C Yellow No. 6, FD&C Blue No.1