Whats happening is that when you set the weight value to 0 maya will need to assign a joint or joints influence over that vert.

So when you do not hold the weights it will just re-assign it to the joint you just removed the influence from. But when you do hold your weights maya decides another joint to assign that vertex to.

To get around the problem instead of stripping the value which forces maya to make its own (wrong) decission as to which joint or joints the vertex is influenced by, assign this vertex to the bone that it should rotate around.

The way i approach skinning tends to be this:
smooth bind with max influences at 1 which gives solid understandable results usually.

I then hold all the weights (using a script if there are a ton of joints etc) and change the max influnces of the bind up by however many needed for the rig. I then go in and unlock two joints at a time to work on smoothing out the vertexes inbetween.

For example if i want to smooth out the elbow on a character ill unlock the joints that represent the end of the humurous and beginning of the ulna and radii joints and smooth out the solid bind created by the innitial smooth bind settings into a nice blend.