I have seen this, but never got resolution to it. SONAR has no means to track MIDI events "at play" with the transport running, which has often become a thorn in my side. MidiOx is a program I have seen others mention, but I never spent the time to get it to work properly. For me, it seems that any track set to "Omni," regardless of source, is monitoring everything getting fired off (and there is no way to tell what tracks are sending what, sans a monitoring solution).
The only sure-fire way I have found to "resolve" this is to use channels; however, some VSTis fire off multiple channels with MIDI Output enabled. Geist 1 can discretely fire off 11 channels (not sure about Geist 2), so it reduces the number of inputs available for usage (and I hate adjusting MIDI controller channels manually to accommodate this). Channel 13 is the default output from my controller just because of one VSTi now.
It seems that MIDI Output on a VSTi simply puts all output up for monitoring by anything listening to the exposed channels (regardless if a specific source is specified), but not 100% sure on that.