This seems to be the case on the release of 4.5.0 also… some things disappear when i open my application in fullscreen, and there are some strange rendering bugs, that is not present in 4.4.1
Yep, just bumped into the same problem on Windows target. (OpenFL 4.5.1, Lime 3.5.1)
No matter what stage.align and stage.scaleMode are, fullscreen is broken similar to @madneon screenshot.
Also Event.RESIZE is not firing on switching to Fullscreen and back.
Here is a screenshot, at the same time, mouse “sees” game buttons where they should be: