Pain!?

My SO and I don't get to see each other a lot because of his job so when we do we make up for lost time. The sex is still great but it HURTS! A lot to the point I want to cry for the first few minutes then it goes away and then about 5-10 minutes after we're done I feel like I need to throw up. I'm really concerned because I haven't had this at all with him in the past 5 years that we've been together. I know that our, as my doctor put it, bacteria doesn't mix well and I get UTI's about once a year but this is different. We just started TTC a little over 3 months ago and I don't want to hurt the chances of us adding to our little family.