This isn't likely to be a PDC issue (e.g. a plugin mis-reporting its latency to SONAR) because the problem goes away when you bypass the plugin. Usually, incorrect delay compensation persists until you actually delete the offending plugin. Also, AFAIK PDC is per-track and is not applied to left and right channels separately because plugins don't report left and right latencies separately. 
 
This all suggests the problem is within the plugin, or conceivably another plugin that's in series with it on the same bus. Something is causing a delay between the left and right channels, and I don't think SONAR is even capable of that. 
 
You should be able to definitively eliminate (or finger) PDC as the culprit by creating a new project with one track, one bus and one plugin on the bus. The final output should sound no different whether PDC is enabled or disabled. 
 
This is a long shot, but have you verified that the bus interleave is set to stereo?
 
Can you duplicate the problem using only a single plugin? It could be a completely different plugin that's actually causing the problem, rather than the one you remove to make the symptom go away. 
 
If the plugin you're testing is VST3, is there a VST2 version of the plugin you could substitute?