Hi, I f your thyroid profile is back to normal after increasing the medication, you should not experience any menstrual irregularities. In fact, it is the hormonal factor that could be the culprit in causing the cycle disturbance, more than the treatment. If you have been sexually active throughout and have never had this menstrual delay earlier, please get pregnancy confirmed/excluded through a HPT or blood test. You may also need a trans-vaginal sonogram to clarify the issue. So, please see a specialist for a proper clinical evaluation and further management. Hope this helps.