I don't know that I would want to date someone who would do a background check on me. I don't have anything to hide by any means but it would make me uncomfortable that someone was going behind my back to find things out when they first met me rather than just asking me about myself.
I understand that what he was telling you wasn't ringing true to you but if it was me I think I would have let him know that I was interested in researching it further for myself to see if his story did check out. I think that he probably would have just come clean right away if that was the case.
We all have things in our past that we aren't proud of. There are things I'm not going to tell someone in the first few meetings because that level of trust just isn't there yet. I don't know that the info isn't going to be used against me in some way in some other area of my life. This fellow doesn't know you any better than you know him. I believe that people have a right to some level of privacy. Just because you can find it on the internet doesn't mean you have to.
Sometimes it seems that people are looking for dirt on those who they are just meeting so that they have a reason not to trust them right off the bat. Trust is mutually earned. I don't expect 100% transparency from someone who I am just meeting. Just like I don't show 100% of who I am right off the bat.
Everything will be ok in the end. If it's not ok it's not the end.