Hello my friends:
I have a Korg Triton Extreme as a MIDI Controller. The MIDI IN/OUT of the Triton is connected to a MOTU MIDI Express 128 (Channel 3 IN/OUT).

Below is an explanation of my setup/settings.

1. First I add Instrument Definition for Yamaha Motif Rack.
   Edit--> Preference --> MIDI --> Instruments
2. I click define and import Instrument definition for Yamaha Motif Rack
3. The MOTIF is connected on MIDI Channel 1 (IN/OUT) on the MOTU Express and so I assigned MIDI Channel 1/1 through Channel 1/16 for the Motif, as illustrated in the screenshot below:
   
   
4. Next: I create a New Blank Project and Insert a MIDI Track with the below settings:
5. MIDI Input = OMNI, MIDI Output = 1-Express 128: Port 1, MIDI Channel = MOTIF 1
6. In the track Inspector I select a Sound Bank using the available Instrument Definition
7. I select a Patch: Note: I am able to control the Motif Rack and browse through sounds by using the Track Inspector.
8. I play or Record the sound/patch, when I select the Track MIDI Echo is automatically turned on.
9. Next, I insert a second track, this time, MIDI Input = OMNI, MIDI Output = 1-Express 128: Port 1, MIDI Channel = MOTIF 2

 Regardless of channels, both track with play the same sound, even when recorded.
 
Here are additional settings:

Screen shot (MIDI under Project):

 
 
Finally, Playback/Recording under MIDI:
Screenshot:

 
It's been almost a a decade since I mess with MIDI and I feel I just came out of a coma.

Thanks my friends:

AI

So what you're saying is if you select a piano and send on channel one it plays. If you change that channel 1 to a organ you get an organ. But if you insert a new track select a tuba send to midi channel 2 you get the sound selected on channel 1not 2
Is this correct?


In you settlings change you buffer under playback up that to 500 or more. I use 1,000. This has nothing to do with your problem but it's recomended so I thought I would mention this.

sock monkey
So what you're saying is if you select a piano and send on channel one it plays. If you change that channel 1 to a organ you get an organ. But if you insert a new track select a tuba send to midi channel 2 you get the sound selected on channel 1not 2
Is this correct?

Yes, you are correct!
I select an instrument and it plays/record on Track 1, then I go to Track 2 Assigned to Motif Channel 2 select a different instrument and it plays. But If I go back to track 1, I get the Track two sound, so the same sound on all tracks regardless of channels.
The current selections plays on all tracks.

In a nutshell, it seems as if the current instrument selection overrides the previous selection, so each time I insert a track and select a sound, then that sound will play on everything else.

Are you loading a different instance of your synthesizer (MOTIF) for each track into the Synth Rack?  I am not familiar with MOTIF, but if you only have one instance, when you change the instrument the Synth may be capable of only putting out the same sound to all outputs.  You should show MOTIF and MOTIF(2) or something to that effect in the Synth Rack if you have more than one instance of the Synth; set each to the instrument you want.  Each should have its own MIDI input track that is directed to the different instance of the Synth, and each should have its own audio output track coming from the different synth.

MorganT
Are you loading a different instance of your synthesizer (MOTIF) for each track into the Synth Rack?  I am not familiar with MOTIF, but if you only have one instance, when you change the instrument the Synth may be capable of only putting out the same sound to all outputs.  You should show MOTIF and MOTIF(2) or something to that effect in the Synth Rack if you have more than one instance of the Synth; set each to the instrument you want.  Each should have its own MIDI input track that is directed to the different instance of the Synth, and each should have its own audio output track coming from the different synth.

Thanks my friend:
I am afraid I am not certain what you mean by instance.  What I do know is because the MOTIF is connected to MIDI Port 1, it will automatically have access to 16 Channels. Each MIDI Port represents 16 Parts or Channels.
So in my image above illustrating the Instrument Definition setup, the Motif is assigned MIDI Channel as follows:

Port 1: Channel 1:
Port 1: Channel 2:
Port 1: Channel 3:
Port 1: Channel 4:


As illustrated here: (Screenshot)

and so on....

These numbers simply illustrate that Port 1 is assigned 16 Channels.

Now, in my track set up, I am selecting a new channel for each track:

For example:
MIDI Input 1: Channel 1 Track 1
MIDI Input 1: Channel 2 Track 2

Is this what you are referring to?

The MIDI is standard for anything  MIDI so MOTIF will be the same as Roland or any other MIDI compliant device.

I think he thought you were using a VST instrument and not outboard. 
I think your issue will lie within the Motu hardware itself. As the behavior you describe is not what I get when using my Korg 05w But the Korg needs to be in Multi timbral or GM mode to work this way. 
Perhaps the motu is set wrong. 

Cactus Music
I think your issue will lie within the Motu hardware itself.
Perhaps the motu is set wrong.

I do not think so because I just unplugged the MOTU and attached a MIDI SPORT 4X4 (MAUDIO) and I get the exact same problem.

Something is not setup right in Sonar.

MOTIF is hardware, yes? I think I got this one for you. Since we know you're transmitting  and receiving MIDI correctly (you can hear what you record), it's not anything Sonar related. I'm pretty sure you have that right. I believe your problem is due to the fact that you are in VOICE mode and not PERFORMANCE mode. PERFORMANCE mode is where Yamaha allows you to do multtimbral (16 midi ch) Try creating a blank performance (if you have to, initialize a stupid user preset that you know you'll never use, or back it up in the UTILITY or JOB modes.) OR If MOTIF has a GM or XG mode, use that. Now either set up the PERFORMANCE  multi by assigning the 16 or less patches that you want to use to the correct midi channels, or see if you can find a MOTIF instrument definition (Sonar might have one, not sure) and assign from within Sonar. Lastly, don't transmit midi from the MOTIF. You could get double notes from it looping back on itself. If it works, NAME IT, so you have it to tweak for the next project.
I have an EX5r which was MOTIF's predecessor and I'm going off of memory since I haven't used it that way in a long time, but I know I got it working. 

orangesporanges
MOTIF is hardware, yes? I think I got this one for you. Since we know you're transmitting  and receiving MIDI correctly (you can hear what you record), it's not anything Sonar related. I'm pretty sure you have that right. I believe your problem is due to the fact that you are in VOICE mode and not PERFORMANCE mode.

Yes my friend that was indeed the issue: Just a bit of correction, MOTIF has MULTI Mode but that's close enough.
Once I change to multi Mode, just by pressing the button, I am able to assign different patches to tracks on different channels and play with no issues.

You really save the day!

Thank you so much.

Sorry I said Motu when I meant to say Motif, So I was right, it was a hardware setting, not Sonar.