Diode stops conducting. Conducts again after applying higher voltage. What happened there?
I suspect it has something to do with the initial forward voltage when you first apply power, which, because of the caps, will be the full supply voltage. 

Although the S1D-13-F should be able to handle the full supply forward voltage and inrush current to the caps, "should" is the operative word here though. 

You stated "I have had a few of these PCBs stop functioning" which suggests they were working for some time and then failed. That suggests something is getting stressed, and the peak forward voltage and current would be by prime suspect. If it IS overstressing it, then failure mode could be weird. 

Moving the diode to the right of C1 would solve that issue. Easy enough rework to the cap connection too.. Though it does leave the cap open to being reversed, it at least limits the threat.

Ultimately, if it is a real and present danger of reverse connection, a better method is to use a different technique, such as a up diode between ground and 12V and a polyfuse. That method gets rid of that unnecessary diode voltage drop in the line too.

BTW. I would have wired that connector with the centre ground and 12V on both pins 1 and 3. That way it will not matter if it gets plugged in backwards.