Just started with Cubase 8.5 pro and experienced the following.
The click track and metronome are out of sync with the measures on every song. When I try record, say, a hi-hat click track (on the 1-2-3-4) and quantize, it places what should be the first beat on the second beat. So every measure is off by a beat. I tried changing the metronome/click from internal to midi, and the same thing occurs. The fact that quantizing places everything on the same offbeat makes me think there’s something more than just the metronome settings.