I've dealt with this before with a project in which a series of children's blocks roll onto the screen to spell out a word. You have a couple of choices -
1. Assign objects which are not close together to the same set and hope the randomness of the other objects hides the fact that the movement is not all independent. This is what I did with my block project and it worked fine.
2. use two instances of Invigorator, so you have more available sets. The drawback is that the objects from one instance may not look like they're interacting correctly with objects from the other instance. Ig will get tricky as the objects pass eachother in Z space.