Did you make your cubes part of a hiearchy? A reminder, if you make geometry party of a skeleton or envelope, you will be prompted to add this kind of behavior. Any chance you have cubes that are getting keyed as children of a parent you didn't expect, or an evelope?If this doesn't help, perhaps you could give a step by step detail on how to reproduce you problem.
Another thing to try: If you are using local envelopes, you need to freeze them first (doesn't matter their position).
Urp