@mitu That was indeed the problem, using the same emulator fixed everything! Thank you so much, I was going crazy there for a while. Merry Christmas to all of you!

Got it all sorted out.
Fruitbox running smoothly on a Jessie-based RetroPie image, straight from the EmulationStation main menu.
And I wrote a how-to, so you can too.
https://www.raspberrypi.org/forums/viewtopic.php?f=38&t=188723&start=1594
Thanks much for the input @zerojay , it got me pointed in the right direction!

@pjft One can hope. My wife works in the film industry (prop painter), and her current project ends in about a month, so she'll be able to pick up a bit more of the house burden soon.