Ok...we found the solution...and it's kinda ridiculous...so i leave it here:
Leap Interaction Engine has some issues on startUp, when it tries to locate controllers. If the Vive Controllers are off, for example, then it will never find them, after they are turned on, until you restart the level/app
Furthermore, Leap Interaction Engine seems to need some time/has a timing condition on startup...so it really likes to have a splash-screen or anything, that delays the app start a bit. If you directly jump into the VR-Level after starting the app, you will, most likely, end up like us, without active controllers.
Our quickfix was, to re-enable the unity splashscreen with its 5 second delay.
This should really get some attention or at least some documentation please....