I was having a similar issue and couldn't find the answer in any forum or web searches.
I had been experimenting with unfamiliar sounds, duplicating then muting previous tracks for each new performance & sound, so didn't even realize this was happening until I tried going back to one of the first tracks & discovered the original sound had been replaced with the most recent one, as all the others had. The same problem happened whether I duplicated a track or chose from the dropdown when adding a new track from scratch. It also happened if I made a new track and dragged the MIDI info to it.
I didn't want to lose the MIDI info, so after some experimenting I finally solved my issue by choosing "none" on the input selection of the tracks with the MIDI performances I wanted to keep, which unlinked them from the other instances of the same plugin—albeit different sounds—I'd used when recording. (I couldn't necessarily remember which instrument preset I'd used on each of the preceding tracks so tried solving this as I recorded new tracks by naming each track with the plugin and sound name so I could find it again later.)
Then—instead of using the dropdown in the track—I dragged over (e.g.) PresenceXT, etc. to each track from the browser and finally got separate instances that I could manipulate independently. It was tedious to go back retroactively to do this, & then try to find the original sounds I'd played for the existing MIDI parts, but at least now I won't be losing any time in the future if I want discrete tracks.
On the other hand, for something like a drum kit & performance this feature makes it way easier to tweak things. For instance, you can record a bass drum part and duplicate the track (or new track + dropdown) to add each component, e.g. hat, snare, toms etc. to the same instrument while keeping tracks separated—way less piddly to tweak in the MIDI editor too.
