I could repro with X2, so presumably is an issue with X1 as well. I never realized that "mass normalization" created a new WAV,
but did notice that when normalizing multiple tracks, the gain would only increase as much as the highest track would allow - in other words, if one track peaked at -6 and another at -3 and I normalized to -1, they would peak at -4 and -1 respectively. Your experience explains why. As a result, i got into the habit of normalizing individual tracks because normalization doesn't do what you want it to do with multiple tracks, so it sounds like that's what you'll need to do.
Incidentally if you normalize any track in X2, it will create a duplicate edited version. Because this is a destructive process, SONAR has to create a separate temp file in case you want to undo. However because it's a temp file, if you "save as" and specify one file per clip, the temp files go away.
Haven't tried with X3 but will later today.