Windows 10, Loaded an audio file, opened up smart Bypass loaded one plugin (Fab-filter Pro-Q 3 ) I had nothing set in the plugin so it was flat. Played the file and the WL Peak meter shows +3 but the file is at -3 dBFS. I am confused. Got out of Smart Bypass and everything was fine. The file played back at -3 dBFS as it normally does. Did something change between 9.5.5 and 10? Thanks in advance. 
I found the problem: when you open the Smart Bypass Window the 1st time, it works.
It you stop/restart playback, then the original audio signal is not what it should be.
Until a fix, there is a workaround: stop playback by pressing Control (Cmd on Mac) while clicking on the Stop button of the transport bar.