Ths subject of issues with cloning simple instrument tracks has come up before. There was a pretty hot thread on it last summer:
http://forum.cakewalk.com/Why-are-mix-controls-on-cloned-instrument-tracks-linked-m2856182.aspx My conclusion was that the concept of cloning (i.e. two or more tracks of the same type having exactly the same settings throughout but operating independently) is incompatible with the concept of simple instrument tracks (one MIDI track + one audio track + one soft synth all tied together), and should just be disallowed.
When you clone a Simple Instrument track, basically, the MIDI track gets cloned, but it has the controls (and the icon) of the Simple Instrument track from which is was cloned. So you end up with two tracks that have independent MIDI controls, but whose audio widgets control the same set of audio track parameters. Not only does this create confusion, there are some technical problems with the result (e.g. MIDI input echo on the clone can get get locked in the enabled state), and if you split the original, you can't make it back into an Instrument track without first redirecting the output of the MIDI clone.
I could be wrong, but I don't think anything has changed in the interim.