I'm having a similar issue in 10.10.4 -- AM is in a fullscreen mode in the menu system, but when I click on a game to run it, it pops up the dock to show the terminal/exe icon, and the menu bar and window top (stoplight, etc) pops up at the top of the screen. I'm not very good with code, so if it's going to be addressed in the next build I'll just wait, but I wanted to let you know!