It's hard to be definitive as to the circumstances in which this occurs, but I know for instance whenit's in fullscreen and I pause a playing Blu-ray, and then restart it a couple of minutes later, the controls bars (top and bottom) then stay visible.
If the BD-Java coding on the disc doesn't allow mouse actions (so that if when you click on the screen image it brings up an error saying this is not allowed), then it's easy to fix: click on the image of the film in the main part of the window, dismiss the error, minimise the PDVD screen then open it again to fullscreen, and it's usually fixed. If the BD doesn't forbid mouse actions (and so the error doesn't appear), then the only way I've found to put the controls bar back into auto-hide mode is to actually stop the BD playing, exit PDVD, and then relaunch it and restart the BD playing.
Have others seen this problem?