LouVes,
Taking something for a medical problem should not affect your progress with tms work. You're primitive brain knows the truth, so you can't fool it. The brain sometimes latches on to a physical symptom and continues the pain after the issue is resolved. A few years ago I had a minor break in my foot. The break should have been healed in 4 to 6 weeks, but it continued 6 months, until I found Healing Back Pain on my cousin's bookshelf. So watch out for that, lol, don't worry about it, just be aware.
Hope it helps,
Lizzy