Something similar happened to me. I've had one moving violation (speeding, 72 in a 65--A REBEL IS BORN!) when I was 17 and am now 29. I haven't lived in my home state, where I was ticketed, in 7 years. I had no idea it was a misdemeanor, and like the OP, I missed that fact on my Certiphi check. One of my acceptance schools emailed me about it, I changed my underwear, emailed them back and then preemptively emailed the rest too. They all responded with, "Thanks, this happens, we just need documentation of your explanation. We don't expect further issues." I still live with a tiny fear goblin that feeds on unexpected issues, but I think I'm safe.
My points:
1. This stuff does happen, even to careful, intentional people. Things fall through the cracks, especially when you've convinced yourself that you're safe. In the future, trust that even if I am 100% sure that I know 100% of the information on a document going to a prospective boss/school, I'm going to read it at least twice. Carefully.
2. These threads are GREAT, b/c the more that this stuff gets on the internet, the more likely it is that OP's and my brethren from strict states will read it and go 'hm, I wonder if MY state considers speeding a misdemeanor?'
3. Lastly, I know a lot of people consider their pre-med advising committees to be unhelpful, so I'd take this opportunity to improve their breadth of knowledge. I emailed both my post-bacc advising committee and the advising committee of my undergrad from my home-state university to let them know what happened in the hopes that they'll share the wisdom with their students and hopefully avoid, at best, some stressful days, and at very worst, rescinded acceptances.