I am recording a song with several soft-synth parts (strings, mandolin, drumkit) as well as direct recorded audio (vocal, guitars, bass).  The midi parts are being entered from the keyboard or the electronic drums:  when I look at the staff view to make corrections, I am seeing almost everything in double notes on the staff; sometimes triple.  
 
I was wondering if multiple takes were all showing up there.  So after comping, I flattened the comp and deleted the muted takes.  It appears to eliminate some of them; the triples certainly.  But every note is still double.
 
Can anyone point me to why this is this the case?  Online documentation seems pretty thin on this point.   THANKS!

It sounds like you need to set your keyboard so that Local transmit is set to Off

I'm having the same problem -- And, when working with the DAW, the keyboard local control is always off.  Every note in staff view is doubled -- always two notes side by side, with a single stem.  Playback is perfect -- but it makes for very confusing musical notation.  I'm a newbie with Sonar -- has anyone experience this?

I've run into this recently. The default state for MIDI input appears to be "EVERYTHING", which is fine if you are trying to figure out where data is coming from. But if your VI is capable of sending MIDI output (e.g. Kontakt) you will record your MIDI input, and then a few ticks later the MIDI output from the VI.
 
I always set MIDI in to the specific device I'm recording to avoid that problem.

Yes, to ensure that only the data you want is recorded, explicitly set the MIDI input port to the device from which you want to record.  And... if you have MIDI out from SONAR going to same device, to avoid double's you would want to turn off the 'local' setting in the keyboard's configuration (look in manual for where that is, system, MIDI, menu, etc.)
Some MIDI interfaces have built in patch bays that can echo to multiple ports, so check for that as well.
 
Keith

Thanks for your responses.  I'm using the Integra-7 as my MIDI interface.  The MIDI input is set to the Integra, as is the MIDI output.  I always turn local control on my NU-1 off.  
 
The two notes on the staff are only cosmetic.  In playback, even trills sound fine.  And they don't seem to appear in piano roll view.  When I export the piece as a MIDI-1 file, and open it in Musescore (for more detailed editing), the double notes disappear.  When I bring the revised MIDI file back into Sonar, there are no double notes.  I'm definitely a newbie to DAWs.  Are there any obvious settings I'm missing?
 

Check the Event List view; it will reveal doubled events much more clearly and will also show if possibly they are due to the controller transmitting the same events on two or more channels as some controller keyboards will do by default.
 
But it sounds like duplication occurred in the process of comping and flattening in this case. The Staff view cannot hide muted clips as the PRV can, so you *do* need to remove all muted content before trying to edit in the Staff View.

perhaps Cakewalk can FINALLY build a preference for MIDI users to set a default input so many users can finally stop running into this problem.
 
Also being that it is labelled as "NONE" also doesn't help, when it is really acting as a MIDI Omni.

I posted about this here:  http://forum.cakewalk.com/MIDI-Input-of-quotNonequot-Actually-Means-quotALLquot-m3540426.aspx

but all I got from Anderton and others is that I am an idiot and everything I say is wrong.