OK I just tried a simple instrument track, Far as I can tell it works just like a midi track but the instruments is on the same track. Actually seems this would be impossible for the midi to play anything but this instrument! Other than what scook is getting at about enabling midi output which I understood was for using outboard gear so not sure why you would have that set up. It certainly not a default setting.  But You do have virtual controller showing as input which I would change to NONE just to see. 
 
At this point all I can think is you have re named the tracks wrong. Naming a track Cello doesn't mean it will play a cello. Once again check the patch P box and make sure you have the correct instrument patch selected. 
 

 

Cactus Music
 Other than what scook is getting at about enabling midi output which I understood was for using outboard gear so not sure why you would have that set up. It certainly not a default setting.  But You do have virtual controller showing as input which I would change to NONE just to see. 

The default in X3 "Enable MIDI Output" for synths that have the ability. This has nothing to do with hardware. It is the way software arp and sequencer plug-in send MIDI data. Some synths pass through MIDI data others can send data generated in the synth to other tracks. It is also used by VST MIDI FX.
 
One thing to try is set the inputs on already recorded tracks to NONE (or at least something other the All Inputs > MIDI Omni). Keeping in mind when input echo is enabled MIDI and instruments tracks will reset their input to All Inputs > MIDI Omni.

Well, I certainly don't name it Cello so it will play Cello, when I create the track I'm choosing a Cello Instrument plugin (which in this case happens to be called "Container"), I name the track Cello so I know it's the Cello track.

Thanks Steve. I have never used any sort of routing like that so not my area of expertise. 
I notice in his screenshot the inputs are set to Virtual Controller 0. Does that come into play somehow? It's another thing I have no clue what it's for and can only guess. 

Cactus Music
I notice in his screenshot the inputs are set to Virtual Controller 0. Does that come into play somehow? It's another thing I have no clue what it's for and can only guess.

The virtual controller is just like any other controller except it is driven by the PC keyboard. Inputs set to it should only see data from it eliminating the chance of getting data from other sources. I just dawned on me the OP's .sig is not accurate. Tracks set to a specific controller will not change to All Inputs > MIDI Omni when input echo is enabled.

I don't understand midi, so anything those tracks are set to is something the program did on its own. Right now, I'm afraid to even open any other projects for fear that they will get messed up too. However the "Insert Instrument" option for creating an Instrument track chooses is something I haven't a clue about, and I only change it if I'm troubleshooting a problem like this that already exists. And in this case, I have messed with it trying to get the tracks to play the correct parts. I know how to reassign the original Instrument Plugin, but that doesn't affect whether the track is playing the correct part or not. I get the feeling this is something so simple we're all over-thinking it, something not checked that should be or checked that shouldn't be, but I don't know what it is.

 Your just blaming the software? Ya, I realize it's all Greek to someone new to MIDI but we all have to go through the process at some time. And that's by reading, or watching videos. 
 
And Container seems a weird ?plug in?  to use , A quick search for it leads me to beleieve it's a VST container to run VST's in programs that don't support the format..  please try something we know works like Dim Pro or even TTS'1. 
You problem might be this "container"  what ever that is.  
 

Cactus Music
And Container seems a weird ?plug in?

I believe plug-ins made with synthedit use Container as the default plug-in name.

Ahh, yes it sort of looked like a none professional set up and possibly 32 bit as well. 
 
I will wait for a screen shot that shows all the in and out boxes clearly. The synth rack would also be nice. 
 

Hi tindog, check out the previous scook post about "Enable MIDI Output" and check if your plugins have it enabled (in their properties). If yes, try to disable it and check your project again.