High failure rates after pcb coating using DC 3140 RTV
I am going to take an educated guess and suggest that @brahns is probably right and it's related to the process used at your contract manufacturer. Some parts of microcontroller boards (the crystal in particular and sometimes the reset circuitry) are sensitive to leakage on the board and the use of "no clean" flux can totally screw things up. 

There seems to be contamination left on the board that can be affected by moisture humidity and cause excessive leakage. In the case of sensitive instrument boards, the slightest bit can cause problems. Traditional RA fluxes require solvent cleaning (which is a pain for the contract manufacturer, lots of environmental issues) but they're the best. I think water soluble is somewhere between the two.

The contamination is extremely hard to remove- solvent and mechanical scrubbing does it, but it's not easy nor is it cheap. 

Anyway, that would be the first thing I would investigate, and see if they've made any changes to their process recently (of course they may be cagey about it, for fear of lawsuits or other unpleasant repercussions, so you may want to go at this laterally- compliment them on how nice and shiny the boards are or something- did you change anything?, then whack them with the 'we have a problem').