I'm using Nuendo, borrowed from my school. I recorded a midi track with a certain VST instrument and setting. I then duplicated the track, changed that VST's settings and recorded a second track. However, when I changed the VST settings, this changed the original tracks' sound too!

This makes sense as to why, but how can you make the MIDI independent, so it stays the same while you make new MIDI tracks?
MIDI's just a bunch of 1's and 0's. you dont record any sound. you have to keep the sound you want and the MIDI info on the track to hear it on playback. just copy that info onto another track to have the exact same performance run through a different instrument.

if you want to keep the sound and move that around and treat it as audio, you'll have to bounce it down to an audio track.