Okay, I think I might have found something to try.
In Console View
Click on "Options"
"Meters"
"Track Meter Options"
Select "Pre Fader"
You can also check your busses if needed
Hit Play and check to see what your level look like there now.
If any changes are made you will need to go back and recheck any settings you made on any tracks to plug-ins.
If the levels are good dont forget to set it back (Post fader)
One thing you will notice is the meters and sound do not effect each other. Meters will display regardless of fader position on what Sonar has captured on the recording.
Note-I just stumbled on this last night and posted a comment in "Coffee House" on it. Id set all my levels etc.. to what I thought was correct without ever thinking to see (Prefader) after recording what X1 was thinking was captured. There was a huge difference for me and Im trying to figure all that out now.