Same thing is happening to me still on a N3DS (I am using the latest version of Luma and B9S for my CFW. I am also a version behind the latest N3DS firmware update).
I am installing the three .cias, the launcher .cia, and using the latest nds-bootstrap v0.9.1 (REV 01). Quick start still doesn't allow me to use the touch screen.
I have deleted the nds-bootstrap.ini file and allowed it to be recreated, but no go. I have gone through different bootstrap versions but no go. This is getting a bit disheartening that others are able to get it working on 3DS but everything I've seen other people try has yet to work. The touch screen will just not work when quick start is enabled no matter what I do. New bootstrap, cleared out .ini file, reinstalled every .cia, absolutely nothing is working for me.
I am able to use touch when turning off quick start and starting the game up from the DSiMenuPlusPlusLauncher via last loaded ROM. Quick start has never worked for me from when I initially installed. Anyone have any other ideas of what I can do?