I have these types of flucuations too. I started seeing my endo in Oct 2009. My Lyme doctor had me on too much levoxyl and it was totally suppressing my TSH so the endo had to start from scratch.
She first took tests to see what my levels were and then started lowering my levoxyl. My TSH since October has been all over the place from a low of undetectable to a high of 5.78. I had been on the same dose at the time it was 2.01 and that is when I feel best. But then she tested 2 weeks later and it had jumped to the 5.78 for no reason.
So she increased my T3 at that time. Now in July my TSH was 2.88 and so she has now increased my levoxyl to .44mcg.
I am currently on 1 pill of T3 and .44 of levoxyl and am due to get tested again in 4 weeks. She has no idea why it isn't stable even though my doses are not changing...
She also tested my T uptake and T3 and T4 free..