Using a guide to get blu-rays to work with VLC (might not be legal, google search: "Play Blu-Ray with VLC in Windows", second link) I was able to get good playback (ie no missing frames)
I will double check this tonight when I get home from work, but I know it was working without any noticeable skipping. When I tried to get AnyDVDHD to overcome the protection I got the same problem.
As for the sound skipping, I get the same thing over USB headphones (the entire controller is being passed through). I will try the cpu reservation and see if that helps at all.