I wish I could tell you what is happening, but I stopped using the Customize the Ribbon Dialog quite a while back. I can tell you that changes to the QAT are also stored there by default these days. They used to be in a separate file.

If this is sufficently annoying, use the XML modification methods and store in a separate global template (not normal.dotm).
Customize the Ribbon (It doesn't take rocket science) by Greg Maxey, MVP
RibbonX: Customizing the Office Ribbon by Robert Martin, Ken Puls, and Teresa Hennig

I've never had problems with those modifications moving around.