Sanderxpander
Did you even bother to read my post Craig?! I get so tired of these workarounds for real issues...
Actually I'm just messing with you, that sounds like a really nice solution. By FX rack do you mean that track's FX bin or some other new feature that I've missed?
Having separate midi for each synth is actually preferable to me so that's not a problem.

I've never run an actual synth from an audio track fx bin (if that's what this is) unless it was a synth that had a function for that specifically (like Z3TA+ FX or Reaktor). Is there any reason why this might be a problem? Will it still show up in the synth rack (which I never use btw) or is it now completely tied to the fx bin? And can I simply select it as a target for my midi tracks or do I need to tick some boxes?

In any case, thanks! I still feel it would be more "elegant" if this worked directly on simple instrument tracks (because the assumption is that you clone the instrument track, not a bunch of references to an external synth) but from Sonar's logic I understand why it's not the case and this sounds like a really good solution!

Now be honest, did you think for about five seconds that you got shot down again? ;)

Actually for about 1 second, but then even before hitting the next sentence, remembered your sense of humor was not surgically removed at birth  
 
I'm getting used to it. Some people just like to spin things in as negative a way as possible. Although I would think they want to change, they apparently don't, and there's nothing I can do about it. So, I'll communicate with those who like to communicate, and let others project on me the faults they see in themselves. Anyway, to your questions...
 
it used to be called the FX Bin, now it's called the FX Rack, probably because it looks more like a rack these days. Sorta. Or maybe "bin" sounds too much like trash bin. 
 
I thought no way it would show up in the synth rack, but I tried it and...whoa!! It shows up in the synth rack.
 
There are no known issues with doing this. This was the way it was always done but people found it confusing, so Cakewalk created the instrument track thang.
 
You can select it as a MIDI input for a MIDI track's output.

Cool stuff! Thanks!

Hi Craig,
 
Sorry for not getting back to you earlier about this but at the time I was otherwise occupied and I only just ran into a similar situation where I wanted to clone a synth. I tried your instructions but I couldn't drag the synth to the fx bin. In fact it doesn't seem I can drag it anywhere at all. I'm confused as to how you're managing it. The synth rack doesn't give any cloning options either unfortunately.

I just tried it, you can't drag from the synth rack, you need to do it from the Browser (plug-ins > instruments). Or you can right-click in the FX Rack and insert the synth that way.

Oh right from the browser. So I would need to do that from the start, no way to "clone" an existing synth in the rack. I feel a feature request bubbling up :)

I absolutely wish clone did what people want (new instance), but it does actually make sense in context when a synth is in the rack: in this case, the synth is "free floating" and it's its output that is associated with the track, not the synth itself, so cloning the track clones the input setting.
 
Compare the case when you clone an audio track with a physical input - you get a new track with the same physical input (not a new physical input that SONAR has managed to create magically :-)).