How do i stop it.
Use the (desktop) Default Programs app and make any browser except Firefox Nightly your default browser then Nightly will always open as a desktop app. If you keep Nightly as your Default browser it will still open any link shortcuts in Desktop mode it will only automatically open imbedded links in Modern UI. If you want to run Nightly as a desktop app just put a link on the desktop. I recommend you don't put Nightly on your task bar because it seems a litte tempremental especially after an update. I am guessing there are still issues with the Nightly install? Remember Firefox Nightly is alpha code and is never going to be as stable as the current release, Stay away from Start Page links as far as possible and everything should be as you want it?
Edit: Find and install the (unofficial) 64 bit version of Firefox Nightly, it doesn't support Modern UI at all and is as good if not better than the 32 bit version.