Some soft synths or even some instruments that load into something like Kontakt, do weird things with regard to midi volume or pitch, or other aspects of the sound, and it can be QUITE maddening to debug and resolve.
I found that some soft synth components of Native Instruments Komplete 8 Ultimate by default have their master volumes tied to CC 11 midi messages - that is something I would never myself do, but it's how a bunch of their components and some individual presets within a given synth are set up.
Certain loaded presets for certain loaded Ensembles in Reaktor 5 have pitch tied to the modulation wheel - which until I figured it out drove me NUTS for almost 2 weeks.
I used the above only as examples of some of the weirdness that does exist out there with soft synths, so let's start by figuring out exactly which synths and which presets you are having these issues with.
Oh, another thing that could be at play here is some of the Sonar settings, like that midi buffer setting talked about above (250 ms being too small for some folks, etc). The default setting for that used to be 500 ms, but in one of the X releases of Sonar, it got changed to now default to 250 ms. Another Sonar setting to look at is the one that defaults to Always Zero out continuous controllers when project play stops. If a synth or preset for a synth, has volume or pitch tied to the modulation wheel, that could jazz up your track's volume even though you wouldn't see any recorded midi event data related to volume to account for such a loss of volume.
And, for my particular issues with some of the Komplete 8 Ultimate synths, either at the synth level, or in some cases at the individual loaded instrument level, there were option defaults I could change to sever its default of tying the synth/preset master volume to CC 11 changes. THAT fixed a BUNCH of really weird volume changes for me.
Can you elaborate on what precise synths and presets you are having these issues with?
Bob Bone