I having some problems with how the CMSDesk and CSSSiteManager display. Sometimes all the info will display after one click, sometimes I have to click several times to get navigation, context, links, etc. to display. And this is not just for the frame that has the content it is for everything on the page. I've tried compatibility view and it helps a bit but doesn't always display everything correctly. I can email provide screenshots if you desire and give some of the actions I was performing when this happens.

I also have problems if I have the CMSDesk open in one tab and the CMSSiteManger open in another tab and if I make changes to say a webpart and go back and configure it on a page in the CMSDesk, it won't save the changes, it just gives me a blank popup window. Same is true if I modify something in the CMSDesk and go to the CMSSiteManager and modify something like a Document Type or some site settings, unless I navigate directly to that place I want to modify when I switch over to the site manager it won't save the changes I make. I had no problems doing this in versions 5.x or lower.