I remember having a similar issue in Reaper some years ago with Kontakt.
Each start of transport send CC07 and CC10 on every midi channel as I remember, being volume and pan.
A feature on track panel was activated to make faders run midi.
So setting in Kontakt was destroyed each time transport started.
Is there something like this in Sonar? In Sonar 4 there was something as I recall, when selecting a midi channel also activated fader for midi volume.