Check the linkage that I have pointed out with the red arrow, when the primary throttle plates are closed it should be snug.
The vacuum secondary diaphragm spring will push the secondary plates closed but there are several tension levels available for those springs and they mostly determine how quickly the secondaries open, not how well they close. This linkage is what's most responsible for making sure that the secondaries close with the primaries. It can be bent one way or the other (I just use pliers or vice-grips) to make sure that they are closed but NOT holding the primaries open either. If this is set right, the secondaries are subject to the same return spring pressures that the primaries are and should solve any problems like that. Hope that helps.
Steve