After wasting several hours, I'm about to give up. 
 
I wrote and recorded a song with MIDI and audio tracks. Plays fine, but since I needed to extend the intro 8 more bars to line up with a video, I thought I would just cut and paste the first 8 bars and have it move everything over. Sounds simple, right. 5 minute operation.  WRONG! Sonar totally messes up all the tracks. I checked to make sure I had all the right options selected in the Paste Special. Ugh. Maybe it is time to move on. 
 
 

Sounds like you should be copying and pasting instead of cut and paste.

This feature has always been a big mess just waiting to happen. Ripple editing is supposed to be what you use know but I've yet to figure it out ( lazy) But what I do,,just did this last night to add an extra verse,
 
Make a SPLIT across all tracks in the places that make the beginning and end of the part your copying. Use Ctl A to select all tracks and make the SPLIT making sure it is at a measure ex: 3:01:00 
 
If the part you are copying is 12 measures
Drag the right hand part of the song that will come after the paste to the right 14 bars out of harms way. 
Now copy past int the blank space the 12 measures you want
Now drag the rest of the song back to where it belongs
 
Super clunky but that's my work around and it never fails.. Because I've gotten good at it I have not tried riple editing. 

If it is messing up all tracks, maybe ripple edit is enabled.
If it is messing up all the MIDI in the track is could be Preferences > Customization > Editing "Slide Over Old to Make Room" is selected. Use one of the other options.

there is a difference between selected and focused.
You must have the paste track selected, not just focused (click on the track number to select it).

I was doing a copy and paste. 
 
Lesson learned: A better technique is to use the Project - Insert Time/Measures option. That will clear out the necessary number of measures and move all the other tracks out of the way. Then the copy and paste special works fine. 
 
Thanks for the feedback. 

There you go, there's always 6 ways to do the same thing in Sonar. We use what works for us.