Please clarify a couple of issues:
  1. You indicated that you have many boards on which your software runs perfectly.  Are they the same make, model, and revision as the problem board?  Is it only the controller board that has changed or are you working with other unknowns (i.e. power supply, peripheral boards, cables, etc.)?
  2. Have you ever seen these problems before this board?
Intermittent failures as you describe, usually fall into one of three categories:  interrupt related (asynchronous interrupts stepping on each other), thermal (defective component or bad solder joint), dirty power (AC noise getting through power supply, defective or failing power supply, intermittent connection on either source or feed side of power supply).
 
Paul R. Cormier