i have just been diagnosed with auto-immune hypothyroidism and ha...

i have just been diagnosed with auto-immune hypothyroidism and have been prescribed 25-Eltroxin sodium. I've also been trying to conceive. At the time of starting my medication I was coming up to ovulation. On day 13/14 of my cycle I was worried as I noticed significant breakthrough bleeding (bright red/with clots). I am waiting for my temperature to go up to show that I've ovulated but it hasn't happened yet. My bleeding is lighter now, 5 days on and brown in color. Can anyone explain how/if thyroxine can cause this as I've never had mid-cycle bleeding before. I have been bleeding for 4 to 5 days now and its not as heavy as it was. What is happening to me?