Zen, I take a fairly high dose of Levoxyl (I alternate .175 and .200) and haven't noticed any effect on my daily exercise and HR. We're all different though, especially when it comes to meds!
I have noticed, though, that a 2 - 3 week layoff has a huge effect on cardiovascular conditioning in most people. If that is what's going on with you, be assured that it comes back quickly. But don't be surprised if it takes a week or more of pushing a little farther each time to get back to your half hour on the elliptical.
My suggestion is to keep doing the elliptical for a week and monitor your HR and endurance each session to see if it's the meds or layoff that's affecting you.
Good luck!