I have a fix to the end action (your first question). You can fix it by changing the duration of the clip in the XML file that Encore creates. It turns out if you change the duration (I just removed the decimal in mine and rounded off to whole #) - it will work out. Just open the xml file, find the reference to the offending video/menu and change the duration. Doing this fixed this problem for me and the clips always returned to the menu after playing.
As to your second question, I have the same error but I can't find a solution to it. It's possible that Flash cannot encode setting a button to be highlighted as an end action; there are limitations for similar things listed in the guidebook. But if someone is able to do this, I'd love to know too!