mattp Yes, this is known issue. There is a bug report on github with two potential work arounds. Doubt it will be fixed for v35, but at least there are workarounds. Either make a dosbox.bat with the name of the ,exe you want to run or edit the config gen with a small hack to make the GUI work correctly.
The configgen is /usr/lib/python3.10/site-packages/configgen/generators/libretro/libretroGenerator.py and after making the edits, need to do a batocera-save-overlay.
Or, just use the dosbox.bat fix, it is way simpler!