Not sure I'm on the page, but let me take a whack at this...

When you make a morph and activate it, the base mesh is deformed. When you make an additional morph and export it, you are exporting the sum of all changes made... that is morph1 + morph 2. When you reload morph 2, you now have morph1 (already active in the figure) + morph1 (in the exported morph file) + morph 2 (the new morph.) Try turning off morph 1 and see if that doesn't solve your problem.

If it does, then here is how to do what you want:

Make morph 1.

Save it.

Activate morph 1.

Create morph 2.

Turn OFF morph 1.

Save morph 2.

You will now have two morphs that will behave independently of one another.