Thyroid Antibodies/Autoimmune Issues?

I was diagnosed with Hashimoto's thyroiditis a few years ago based on a blood test showing higher than normal thyroid antibodies. I've been on synthroid for a while and my TSH seems to be under control, but I can't help wondering if this autoimmune issue explains why we haven't been successful yet. 

Anyone else in the same boat or dealing with other autoimmune troubles? What has your RE said about them?