I just ran into the same problem along with this problem at the same time:
I try to find it on Techgara and Retropie and I think they are related. Has anyone else noticed the autoscroll right after you exit, and the screen goes black? That is what was happening to me. It would make sense that the "scrolling on exit" controller bug is causing the "black screen on exit" bug for the Slide transition.
Here is what I think is happening. ES fades out it's background graphics as it starts retroarch. The player plays retroarch. The player exits retroarch. ES goes to turn the fade value back up, but is interupted by the autoscrolling controller. ES thinks everything is normal (you can still move around and select other games etc.) but it's screen is still faded. The reason why the fade transition fixes this is because when you switch systems this engages that same fade variable and turns it back up to 100%. Fix the controller bug, and you fix the black screen bug, and can have your slide transition again. That is also why having multiple controllers plugged in would multiply the chances of this happening. 🙂
Unfortunately, to fix the controller bug you have to recompile the kernel with some patches, solution found here:
I imagine this will be fixed in future builds. It should be a fairly easy fix, especially since the patches are already written.