Think of it like this
Track one is using the VST for Organ
If you assign the same instance of that synth then set it to Guitar, that instance of the synth is now assigned to guitar.

It is possible to create another separate instance of the synth by using the Port option Jeff mentions.

Unless your VST is a multitimbral synth, that is how it works.
If it is a multitimbral synth and can use different sounds on different MIDI channels, then you could try assigning MIDI channels, but you didn't mention which particular VST Synth (VSTi) you are using, so it's hard to get more specific.

Make your sound your own!
.. I do not work here, but the benefits are still awesome