RedSkyRoad
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.

Yes, I can replicate it without fail if I do as you describe. I think perhaps you omitted the following: "then convert into a Groove Clip (ctrl+L) before copying. Next, Paste Special with linking." 

icontakt
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. 

I don't understand. Shouldn't moving up, moving down, or transposing ONLY move notes vertically? Under what conditions would transpose, or move up or down, move notes horizontally? 
 
Transpose, Nudge 2, and Nudge 8 work here as I expect them to work, so I'll need steps to reproduce in order to pursue this any further.

I think the OP is saying that the notes in the linked clips move horizontally. At least that's what happened when I followed his steps.
 

RedSkyRoad 
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

Maybe this will make the issue clear. In this video, I move the blue notes by dragging, and then move the red notes by Transpose.
 

RedSkyRoad
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!!!!

I'll try again in more detail. SONAR assumes a MIDI clip begins with the first MIDI event - note, controller, whatever. You want SONAR to assume the beginning of the clip is where you want it to be, but SONAR has no idea where that is (a quarter note, a measure, or whatever before the first event). It can't read your mind, and there's no data to give it a clue as to what you want.
 
If the clip starts with data, then both you and SONAR agree where the clip begins and you don't need to hit ctrl+L. But if it doesn't start with data, then you need to tell SONAR where you want the clip to start. One option is to insert any piece of data, as BobF mentioned. Another is to use one of the two methods I described.
 
Now, SONAR could just assume that the nearest measure before where a note starts is the clip beginning, and certainly for most EDM, would be right most (if not all) of the time. I wouldn't be surprised if a program like FL makes that kind of assumption, or bases its decisions about what's a clip on grid position instead of data position. However, I believe the reason why SONAR is data-based rather than grid-based is because SONAR recognizes that many people do not always cut MIDI to the grid. Sometimes you need to link clips with timing offsets, sometimes you need to align to measures and sometimes not, you might want the clips to repeat at a regular interval or not, aligning hit points to video is absolute time-based rather than musical time-based, and so on. You might want to repeat clips over and over again where making one change makes changes in all the clips, or repeat them over and over and be able to make subtle alterations in individual clips without affecting the others.
 
SONAR allows for all these options, but that means a steeper learning curve. If you know what the options are, then you can choose the one that's most pertinent to your style of making music, and to specific editing needs.
 

icontakt
Maybe this will make the issue clear. In this video, I move the blue notes by dragging, and then move the red notes by Transpose.

 
Again, I think the issue is the blank space before where the note starts. If I do what you do, it behaves as you demonstrate. However if I slip-edit the beginning and create a Groove Clip to tell SONAR the clip does NOT begin with the first event but with the blank space I defined, it works as expected and maintains the offset in subsequent linked clips between the first note of the event and the space before it.
 

I'm only a user and see everything from a user perspective. I think any user (especially new users) would find that behavior unexpected, because what the three methods (dragging, nudging and Transpose) are doing is basically the same: select notes and move them up/down. Even if it's not a bug, I would change the behavior if I were a developer wanting to make its daw as user-friendly as possible.
 

I think Craig gave two excellent descriptions of how MIDI is used in Sonar. I look at a MIDI clip as a one off sort of thing. It is a discrete and independent container of MIDI data. It can be a single bar or an entire track. Where a MIDI groove clip is meant to be looped. That is repeated many times. The two are very useful for different reasons. I think Craig made this clearer than I have seen anywhere else. 

Also there was a time in Sonar when there were no MIDI groove clips. 
 

icontakt
I'm only a user and see everything from a user perspective. I think any user (especially new users) would find that behavior unexpected, because what the three methods (dragging, nudging and Transpose) are doing is basically the same: select notes and move them up/down. Even if it's not a bug, I would change the behavior if I were a developer wanting to make its daw as user-friendly as possible.

 
Although I agree in principle, this issue occurs only when linking clips and if the clip doesn't have a defined beginning; the reason for that is so that advanced users aren't hamstrung. A selling point of Ableton Live is that they've restricted MIDI to the most often-needed operations to suit the musical genre for which Live was designed. I don't look down on that at all - on the contrary, I've always admired the way Ableton has remained totally true to their particular vision and design philosophy.
 
OTOH SONAR is intended to be a full-function DAW that can handle just about anything you can throw at it. As a result that means complexity, options, and a learning curve. In fact, while checking this out I found there's yet another solution that causes transposition etc. to behave exactly as you and the OP want, and it's by specifying where the clip is supposed to start in the paste dialog rather than with the clip itself. For example...
 

 
In this case, the first note doesn't start on a measure boundary but starts at 1:02:038, and the clip doesn't end at a measure boundary but ends at 1:04:058. So, in the Paste Special dialog, we want linked clips to start at 2:02:038 (remember you do not want to past a link into the original clip!), and align them to measures. So now the linked clips start at 2:02:038, 3:02:038, 4:02:038 etc. Because SONAR now knows where the clips are supposed to begin, when you transpose all the notes transpose properly, and maintain their correct relationship to the grid.
 
I agree this is pretty deep stuff, and it's understandable people will not read the help but just want things to work the way they expect them to work. But, SONAR will only learn how you work if you tell it how you work. Maybe someday analytics will solve that, but meanwhile, one needs to learn how SONAR works, and tell it what it needs to know.
 
Remember I'm a user too; I don't know code. But, the way SONAR works seems logical to me...if it doesn't know where a clip starts, it can't act appropriately. That's why when this thread surfaced, my first reaction was "you need to tell SONAR where the clip starts." I always just used Groove Clips, but in the process of answering, discovered two alternate options.
 
I'm sure there are ways to simplify Paste Special and linking, but I think the real culprit is that the documentation needs to explain the many ways SONAR can accomplish functions in a more transparent way, and be very specific in terms of illustrating what option you would choose to accomplish a particular task. For example, I don't think there's anything in the documentation that explains how to handle Paste Special with linked clips if the clip's physical beginning is not the same as the user's desired beginning.