I also have 2 instances of the same plug in & according to the properties, path & the ID number the plugin is identical & being listed twice. This has nothing to do with Mono, Stereo, or Multi out plugin.
Since all of my plugins reside in a folder called "C:\Audio" I created a new folder called "C:\Audio-X" where I place a limited amount of VST plugins so I could experiment with this quicker. I performed a Scan of "C:\Audio-X" with both Sonar X3 & Sonar 8.53 with identical results. They both reported the same plugins twice. Here's a sample.
D82 Sonic Maximizer VST ID 1934451064
D82 Sonic Maximizer VST ID 1934451064
Addictive Drums 2 x64 VST ID 2017543218
Addictive Drums 2 x64 VST ID 2017543218
Ample Guitar T II VST ID 1097299059
Ample Guitar T II VST ID 1097299059
WTF is going on?