IDML was never a perfect way to save back and if it’s perfection your need and f you know the target is CS6 users then that is the version you should be using.
I completely agree. If I had known this was going to be this big of a problem, I never would have upgraded. What I find interesting though, is that this wasn't a problem a couple months ago. I don't know what changed (maybe upgrading OS?) but this problem was not presenting itself until most recent. Before the IDML's were behaving atleast rationally and not moving master page items. But thank you for the reply nonetheless.
As a CC subscriber you are entitled to install and use CS6. You should do so. This is exactly why people warn that IDML interchange causes problems, and why it should never be part of a regular workflow.