First, modification of the QAT is simpler if you are doing it within the UI. Modifying the QAT and Ribbon in Microsoft Word.

I'm afraid I abandoned Ribbon Customization within the UI sometime ago because manual customization gives so much more flexibility. I do my editing using the Custom UI Editor. Using that, I've never experienced the problem you are seeing.

Doing the editing with the UI, the controls are shown in order in the Interface and you are able to move them up and down (right and left on the ribbon). Are you not seeing this or is it not keeping that order? What I am reading in your question is that both the order on the ribbon and the order in the ribbon modification dialog is changing. Are you perhaps changing the order using the XML Notepad directly?