I started encountering the same problems you described using Adobe CC Encore in a video project that has 40 video thumbnails buttons. Encore loses the motion menu renders and the links that relate to BD and DVD transcodes everytime I reopen the Encore project. I have to rerender the project everytime I reopen the project, which is a very long process. I also am using WIN 7 Professional.
On another note, has Adobe fixed the loop point pause during BluRay playback? That is one annoying bug. I have been complaining for about 3-4 years about that one.
Encore still isn't ready for prime time.
