it's working! but it mgiht have been my fault all along, I was running it in DSI mode (which was the default)https://github.com/DS-Homebrew/TWiLightMenu/releases/tag/v26.0.1
This is the one I am using, don't know if that makes any difference though, and on the sd card:
sd:/cs3d2d/
sd:/Config.dat
sd:/roms/nds/Cave Story 3D2D+(DS).nds
I also allowed slot-1 sd card access in the TM++ settings (which might not be needed but hey, works now!)
thanks for your help