Hi Folks:
Trying to edit a multitrack master - audio and midi, lots of edited, individual clips per track. When I copy the entire thing (either by command or click and drag) and paste it, it's all out of sync. Any help greatly appreciated and thank you!

You'll need to clarify exactly what you're selecting, where you're pasting it, and in what way and to what extent it's out of sync - milliseconds, beats or measures? Do you have Snap enabled, and with what options (Snap To/By, Landmarks, etc.)? And is it MIDI is out of sync with audio, or both are out of sync with the  audio metronome?
 
Since you're new to the forum (welcome aboard!), it would also be helpful to know your general experience level with Cakewalk/SONAR.

Ctrl + shift key while you drag selected tracks/clips, would keep then in place..

It might help if you explain what your wishing to do? You say a Master? that is normally a stereo file.
If all your trying to do is make a copy of a Cakewalk project just use "save as" and re name it.
If you dragging from another DAW into Sonar then best to have all those tracks start at Zero and depending on the DAW bounce all clips into one long track.
Midi is easy, just save the song as a midi file and then OPEN that in Sonar.. then drag the audio from the other DAW>

Whatever is copied needs to include tempo changes as part of the copy or else needs to be pasted on top of an exactly matching set of tempo changes. MIDI and audio will behave differently in this regard, which a big reason this is important.
 
If just moving the whole thing along the timeline, it might work better to insert empty measures.

Hi Folks:
  Thank you so much to each of you for replying. I will try and provide some context here. I am a longtime Cakewalk/Sonar user, but have cobbled together my own approach through the years, and have not ever really participated much in the online community, or dived to deep into Sonar technical details. I started on 2" tape, so basically use Sonar as a substitute - I run 24-discrete 96/24 audio channels back into my console to mix. Until about a year ago I was blissfully on Sonar 7 on Windows XP, getting fine results. But finally wrangled a new system - fast box from Sweetwater, two new MOTU 24ai/ao's.
   So this track I am working on is typical for me. 50 channels of drums, bass, acoustic and electric guitars, Stylophone and Wurlitzer, plus MIDI softsynth piano and synth, and lots of layered vocals. Still editing - so approx. 20 of the 50 tracks are archived. Lots of editing, so lots of individual, edited audio clips in each track.
   I need to do some big, arrangement editing - shorten a breakdown session by 4 bars, then copy and paste an extra chorus at the end, So: I just want to select ALL tracks from a certain point, copy and insert at a certain point. Won't work. Can't even copy everything and try and paste a second copy after the first (so I could just edit each and join together) but when I paste that copy everything is out of sync.
   This was done to a click - normally, I don't and when editing I just line things up by ear. Snap was not on. Seems to be randomly out differently on the various tracks. The softhsynth Moog patch is frozen (don't have the synth on this new system, so just using the audio. The softsynth piano was not frozen at the time.
   Hey, thanks again for any help, folks - it's funny, I finally bought the new Sonar about a week before the Gibson shutdown, so while not happy to be out all that money, happy to see the new Cakewalk era! Cheers - TB
 
   

Don't know if this relates to your issues, but I had something similar happen. The problem was that when the project was zoomed way out, sometimes I clicked on a clip to move it, but there was a very slight mouse movement that moved the clip in time by a small amount.
 
I could never figure out why the rhythm of the tracks were "fighting" until I zoomed way in and saw there were some slight offsets to the clips. Apparently this happened to some drum tracks, so parts overdubbed to them were off as well.

Timothy Brickley
Hi Folks:
  Thank you so much to each of you for replying. I will try and provide some context here. I am a longtime Cakewalk/Sonar user, but have cobbled together my own approach through the years, and have not ever really participated much in the online community, or dived to deep into Sonar technical details. I started on 2" tape, so basically use Sonar as a substitute - I run 24-discrete 96/24 audio channels back into my console to mix. Until about a year ago I was blissfully on Sonar 7 on Windows XP, getting fine results. But finally wrangled a new system - fast box from Sweetwater, two new MOTU 24ai/ao's.
   So this track I am working on is typical for me. 50 channels of drums, bass, acoustic and electric guitars, Stylophone and Wurlitzer, plus MIDI softsynth piano and synth, and lots of layered vocals. Still editing - so approx. 20 of the 50 tracks are archived. Lots of editing, so lots of individual, edited audio clips in each track.
   I need to do some big, arrangement editing - shorten a breakdown session by 4 bars, then copy and paste an extra chorus at the end, So: I just want to select ALL tracks from a certain point, copy and insert at a certain point. Won't work. Can't even copy everything and try and paste a second copy after the first (so I could just edit each and join together) but when I paste that copy everything is out of sync.
   This was done to a click - normally, I don't and when editing I just line things up by ear. Snap was not on. Seems to be randomly out differently on the various tracks. The softhsynth Moog patch is frozen (don't have the synth on this new system, so just using the audio. The softsynth piano was not frozen at the time.
   Hey, thanks again for any help, folks - it's funny, I finally bought the new Sonar about a week before the Gibson shutdown, so while not happy to be out all that money, happy to see the new Cakewalk era! Cheers - TB

 
Stylophone!  Now that's an instrument you probably don't see in Mixes often.
 
I have to wonder if there is a setting that would preserve the position of the data relative to the cut that you have somehow gotten turned off or perhaps something that auto snaps the data that is set on that you don't want adjusting the alignment of your data.
 

I had this happen a long time ago. My problem was somehow I switched snap setting from "To" to "BY".

I would try bouncing each track to its own clip, so that every track -- MIDI and audio -- contains just one clip. Then do your rearranging. There might be layers or lanes or some darn invisible thing that's not getting included in your copy & paste.
 
In case this turns out to be a bad idea, save a copy of your project first, so you can go back to it and try something else.