I upgraded from 6.0.5 and now all of my audio files (both MIDI and WAV) have a random piano note at the beginning. I also get a random piano note when the program opens. The note isn’t visible in any of the files, and still plays when I mute all of the tracks.
It sounds like you may have some left over application data from the previous version of Cubase 6
First, try shutting down Cubase. Then go to the Start menu, All Programs, Cubase 6, Cubase 6 Application Data Folder. In the top address bar, you should see “App Data (roaming) Steinberg” Click on Steinberg at the top. This will put you in the Steinberg app data folder. Trash any Cubase or Nuendo folder that you see here. This will trash your key commands, preferences, sound card settings, etc. It also should clear up the problem you are having. Restart Cubase. You will need to reset your audio outputs (Devices, Device Setup, VST Audio System).