I have the same issue.
Fresh retropie 2.6 image, kick13.rom and adf copied into /home/pi/RetroPie/BIOS and /home/pi/RetroPie/roms folder and I can verified in SSH that it symbolic linked correctly.
When I start any adf, it gives me a black screen. I can see the process uae4all is running from ps. Thus, it should be screen/framebuffer issue.
May be the only difference is I am using Berryboot. But, I manage to get most of the emulators working, MAME, Atari ST, Macintosh, Neo Geo, GBA, Playstation. THe only one not working so far is uae.