I noticed some weirdness in Nuendo 6.07 when I was demoing the Cubase 7.5 trial.
There seems to be some overlap even though it is not intended.
I didn't experience what you have going on but little things like
the shortcut to route selected channels to the same destination...
Shift+Alt has stopped working in the project window but still works in the mix console.
There were other things as well but I'm still able to work...around them.
This cycle seems to be the "work around" cycle.
Try resetting the mixer and or trashing your preferences.
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