It could be a mental block because maybe you don't feel right having sex with him because your connection was broken there for a bit. Bitter feelings and the sort.
It may sound ridiculous however your self concious does a lot more than you think. Try and figure out if there is anything you are hiding from him, or if you're holding anything against him.

It could be anything from recent medications you've started taking (like birth contol) or any lifestyle changes, stress etc.

It sounds like a completely psychological thing and seeing a doctor might help...But talking with your boyfriend about it might help too.

Is there anything going on in your life now (or has been in the past few months since you've gotten back together) that wasn't present before you broke up?