I used to regularly have issues with Native Instruments components, like Kontakt, FM8, Guitar Rig, and others, where it would override levels every time I would stop and then resume playback.
Turns out a LOT of the Native Instruments have settings set per instrument, that tie the instrument volume to midi CC 7 and 11 messages. SO I would end up having to go into each loaded instrument in an instance of Kontakt in Sonar, and go into the settings change - think it is a wrench, and then to Instrument Options, and then remove the check from the box for reacting to CC 7 and 11 changes.
I don't know if other synths have anything like the above, and it has been a long while since I have dealt with the issue, because I would save/overwrite each instrument immediately after making the changes to basically ignore midi messages to change instrument volume.
If anyone else has awareness that is a bit more coherent and recent and not typed while whizzing through the day on serious pain meds (like I am), please feel free to add to and correct/expand/explain.
I WILL try to look for notes on how I fixed the issues for ME, and will post those if I can find them.
Best of it all to you, and I hope you get past this quickly,
Bob Bone