Ever since upgrading to 3.6, the Map Series functionality hasn't behaved properly. I have a map index layer and several feature classes and annotation feature classes that use page query. If I turn the map index layer off/on or made an edit to the index layer, more often than not when the display refreshed all the layers and annotation will have disappeared. I have to go back into the layout window to the Map Series Pages tab in the contents pane and double click the page I was working on to get everything to refresh. It didn't matter if I was doing edits in the Map view or the Layout view. This was never a problem in 3.5.
Also affected by the 3.6 update was Export Layout. If I spent any significant amount of time doing edits before exporting a map, when I do finally click export the program will stall at "Export in progress." I once left it for 10 minutes to see if it would export, but it never did. As above, this was never a problem in 3.5, and nothing about my APRX changed between 3.5 and 3.6.