swamptooth
Hey Tom,
It's not a bug, it's a feature! 
I looked at the files and yes, there are track header messages setting cc93 among other things in the midi file. Sonar creates by default what Cakewalk calls a General Midi setup measure. This essentially embeds all GM messages like patch changes and GM cc values that occur at the start of the track in the project and hides them in the event list. You can see this because there are programs in the inspector and the chorus and reverb midi controls in several tracks are at a value other than 0 but they aren't in the event list.
You can disable this by editing the ttsseq.ini (found in C:\Users\<username>\AppData\Roaming\Cakewalk\SONAR X3 Producer) file by adding the following line in the [Options] header:
GeneralMidiSMFs=0.
Here's the help page - TTSSEQ.INI
When you add that line, restart sonar, and open the midi file this is how your event list will appear:
Hope this helps!

I just finished testing this out, it worked. Turning off the General Midi setup measure, importing the file, then removing the controllers and playing the track no longer results in the distortion getting zeroed out. There still doesn't seem to be a way to make the setup measure data visible once it's hidden though. I crashed X3e twice doing it though. The second time I saved before hitting play. :)
Thanks!
Hey try this since you have my file:
1. New project
2. Import the midi
3. Event view -> track 5 (the first SQ Wave track)
4. Uncheck notes and delete all the controllers.
5. Bounce track 5 to clips
6. Insert a soft synth (Sylenth if you have it) and route track 5 to it.
7. Hit play.
Do you get a crash too?