Are you able to raise and lower the second set of rows as you go through the field?  Or make a pass with them raised and than another with them lowered.  I'm with Lance on this.  There must be something with how the second set of rows change the way the tractor pulls.  Is the planter mounted or pull type?  I assume the receiver is on the front of the cab roof?  The front end of the tractor can weave quite a bit back and forth without significantly moving the receiver.

I run all mounted equipment.  If I carry too much weight on the hitch or have to drive across the field with the implement in the air the tractor will weave back and forth.