Found a seriously annoying bug.
 
Create a MIDI clip with the first note NOT starting at the beginning of the clip, then create linked copies like in this image:
 

 
Then select the notes in the first clip and drag them ONLY up/down a few notes. NOT horizontally.
 
What happens is that the beginning of clip one changes to where the first note is and then all the linked clips move their notes to the beginning of their clips, ending up on the wrong place in time
 

 
The only way to fix this is deleting ALL THE LINKED clips.

I cant test this out right now, but I will try a bit later.
you can report it to the problem reporter here.
http://www.cakewalk.com/Support/Contact/Problem-Report
 
nice work on the explanation.
 
 

chuckebaby
I cant test this out right now, but I will try a bit later.
you can report it to the problem reporter here.
http://www.cakewalk.com/Support/Contact/Problem-Report
 
nice work on the explanation.

 
Reported.  Thanks for the link.
https://www.cakewalk.com/Support/Contact/Problem-Report-Status/54061
 
PS: Luckily I'm just layering sounds still.  Imaging If I had to redo a complete instrument track.  The UNDO function does not fix this.  It only reverts the notes you moved yourself...

Red -
 
Sonar crops MIDI clips to start at the beginning of the first note/cc in the clip.  I was able to replicate your problem above, but was also able to work around it by adding a PAN CC at 1:01:000 of the primary clip.  I was then able to Paste Special 3 copies as linked clips and edit the notes in the first clip without them shifting.  I'm not suggesting this as a fix.  Just a work-around to keep you moving.  Any CC you insert should work to keep the beginning of the clip from being cropped to the beginning of the first note.
 
I did a quick search to see if there was a setting somewhere to control this behavior, but didn't find anything.  Maybe somebody else will have an easier way to deal with this.
 
Unfortunately, I discovered another bug in the process;  after doing the first Paste Special to create linked clips, a regular Paste via CTRL>V (or via menu) repeats the Paste Special instead of doing a regular Paste.  I will report this as a separate bug.

RedSkyRoadWhat happens is that the beginning of clip one changes to where the first note is and then all the linked clips move their notes to the beginning of their clips, ending up on the wrong place in time.

 

BobFSonar crops MIDI clips to start at the beginning of the first note/cc in the clip.

 
What BobF reported of Paste Special persisting is a bug, but I believe what the OP calls a "bug" is not a bug but expected, replicatable behavior because as pointed out in the second quote, SONAR defines the most basic form of a MIDI clip as occupying the space between the start of the first event and the end of the last event. However there are two ways to tell SONAR you want a clip defined differently from the default.
 
Use Groove Clips. Slip-edit the MIDI clip so it starts at the beginning of beat 1 and ends at the end of beat 4 so they are on measure boundaries, then convert into a Groove Clip (ctrl+L) before copying. Next, Paste Special with linking. This will preserve any "empty" space as part of the clip.
 
With Standard Clips. Suppose you draw an eighth note at beat 2 and a quarter note at beat 3. SONAR's default is that because MIDI data exists solely for beats 2 and 3, the clip covers only those beats. However, what you want to repeat & link is a 1-measure clip that starts on beat 1 and ends at the end of beat 4. So, click on the existing clip to select its basic 2-beats form. Then, drag in the timeline from the start of beat 1 to the end of beat 4. You have now told SONAR that the space you want to repeat & link lasts 1 measure. Copy, then Paste Special with linking.
  
After defining the clip length to SONAR with either of those two methods, I cannot replicate what the OP describes. However note that these two methods are not interchangeable, so you can pick the one that produces the results you want. With Groove Clips, because you've told SONAR the clip itself is 1 measure long, the linked clips will be 1 measure long. With the first method, the linked clips will be exactly like the original - in other words the new clips will be 2 beats long and occupy beats 6 and 7, 10 and 11, 14 and 15, etc. with spaces at the beginning and end of each measure, in between the clips.
 
Three other things:

• Remember to check or uncheck "Align to Measure" as appropriate.
• It seems you can get unpredictable results if you paste a linked, repeated clip into itself. For example, if you have a clip that starts at measure 1 and is 2 measures long, make sure you paste starting at measure 3, not measure 1.
• Because of the Paste Special persistence bug BobF mentions, if you've done a paste special, before doing another one double-check that the settings are as desired.

Good info Craig.  I tried a simple stretch/bounce to clip(s) to get a fixed size MIDI clip, but I didn't try it as a Groove Clip.  Much simpler - I knew somebody would have a better answer.
 
 

BobF
Good info Craig.  I tried a simple stretch/bounce to clip(s) to get a fixed size MIDI clip, but I didn't try it as a Groove Clip.  Much simpler - I knew somebody would have a better answer.

I almost always use Groove Clips instead of standard clips because then MIDI behaves more like audio clips, which recognize silence as "real." As far as MIDI's concerned, if there's no data, there's...no data. But SONAR can tell MIDI otherwise.

I think the behavior described in the original post is a bug, because if you move the notes by Nudge (hit Num2 or Num8) or Transpose (Process -> Transpose), the notes in the linked clips only move vertically. 

Anderton, I always drag the beginning and end of my MIDI clip bigger to span the whole bar but that space infront is NOT kept when I move the notes.  Hence the issue I have.  Please explain your "Standard Clips" method again because it seems that is exactly what I've always been doing - plotting notes and then dragging the two ends bigger to make a measure and then copy/paste.  This does not seem to be working as in my original message. If you follow my steps, you'll replicate it without fail.. I copy linked clips by ctrl-drag

What make a Groove-Clip special above a standard clip and why are there two?  Cant I have it create Groove-Clips by default or do I have to Ctrl-L EVERY time!!!!