Similarly I was a long time staunch atheist. while studying computer science, I worked on a simulation to demonstrate the power of natural selection.. Lots of problems emerged that I had always dismissed when given as arguments from skeptics. More and more heavy handed tweaks were needed to make the simulation produce the desired result- even in the best of circumstances.. That's obviously very brief, anecdotal, inconclusive, but at the very least I proved to myself that the process was not nearly as inevitable as I'd imagined, and as I think many people do.
I think perhaps like Newton's formerly 'immutable' laws, evolution appears so elegant, complete, problems in the details are easily dismissed as aberrations.