I used SONAR X2 Producer as a sequencer to play my MIDI Format 1 files.  When I mute one track, let's say the vocal track of a given song, and then SAVE the file or song with such track "muted", it appears unmuted when I reopen the file again.  In other words, the muted tracks are not permanently SAVED.  I had this same problem with SONAR X1 Producer.   In addition, when I open the midi songs the files open "minimized, I would like to open them MAXIMIZED.  I'm not talking about Sonar, the software opens maximized, the problem is with the files.  Can somebody tell me what I need to do in order to have this feature as a permanent preference?

Welcome to the forum! Are you saving your files as MIDI format 1 files or as cwp files? The reason I ask this is that a MIDI file only saves track/channel/note data, and is not project specific (i.e. can save no information on how SONAR was using it). In order to save SONAR preferences, it must be saved as a Cakewalk Project (cwp) file.

Yes, I'm saving the files as FORMAT 1, not as CWP.   I'll try saving as cwp.  What about if I save the file as .wav (audio format to play with Virtual DJ).  Does the muted track is saved using .wav?

The cwp file is specific to SONAR, which allows SONAR to remember the project view, track specifics, FX, settings, etc. It is akin to a container. Inside of this, it points to audio data files (but does not contain them unless saved as a "bundle file"). The cwp file is pretty small, but saves with it all of the settings, views, etc. that are specific to your SONAR project when it is saved.
 
A nice thing that was introduced is per-project folders (Edit->Preferences->File->Audio Data) "Use per-project audio folders"... what this does is make it easy to find audio you have used for each project. The cwp file does not specifically "contain" these, but points to them when SONAR opens that project.
 
Try saving the file you are working on as a cwp file (when you choose save as... it is the "Normal" save as type). This should resolve your muting issues (and much much more). A project file remembers a lot of settings you have been changing as you work so you can pick up right where you left off.