I'm going to guess it is not planting/planted in those areas and suggest that it will be an implement lift switch problem.  I had the same issue last spring on my first field of soybeans and could never track anything down.  After that it worked fine for the next 1,800 acres so I didn't think about it during the off season.  This year it worked fine for the first 400 acres and then started being goofy again.  I eventually tracked it down to a broken wire on a lift switch.