I have several item farms with hopper minecarts that are on powered rails that should loop infinately.  These carts seam to disappear randomly.  Until I started monitoring this situation.  While keeping track of this issue.  The issue seams to be caused outside of the game.  I have discovered this happens when the game crashes or when you close minecraft using the windows close button (X).  This issue as I stated is random and hope this information can help point you in the right direction to help get it resolved. 

This seams to be a recurring issue that has not been fixed.