SONAR 7 to Platinum a week before the shutdown? That explains your issue here... you just have really bad timing.
 
Sorry; clouldn't resist. 
 
So when you copy and paste everything at once, do the clip start times remain aligned? If contiguous audio clips start together, they are going to play in sync with each other, even if there are tempo changes in the region to which you pasted, but unfrozen MIDI could get out of sync with audio because it will follow the tempo changes. And the start times of non-contiguous audio audio clips could also get out of sync because they will follow the MBT with tempo changes. Other than that, I can't really think how anything would get out of sync in that scenario. Definitely check for unintended tempo changes in the timeline.

I have yet to use this feature, But does not RIPPLE EDITTING solve the old buggy copy paste issues?
 
I have come up with my own workarounds but re arranging a song has always been a huge PITA.
 
One day I will try Ripple to see if it actually does what I hope it will do.
 
 
First all tracks need to be split at the points of entry and exit.
I use SELECT ALL and use snap to grid making sure the split is at a Whole measure 0 point
Now my workaround.... Pasting into the middle of a song always made a huge mess ,, so I will spilt and slide the end part out of the way of the paste.. I always leave a few extra bars of room so if the paste is 12 bars I slide the ending ( right hand part)  over 14 or 15 , paste, then drag the end ( right hand)  back to the end of the inserted ( left hand) part.

Cactus Music
I have yet to use this feature, But does not RIPPLE EDITTING solve the old buggy copy paste issues?

Good point, Johnny. The OP should, at minimum, check to see if Ripple is on or off. This might be the whole problem -- it was for me the last time I was rearranging all the tracks in a song.

Ripple Editing does work much better than the old 'Slide Over to Make Room option', which has been broken for a decade at least. For some reason it's still present in Drag and Drop options, and should be changed to 'Blend'. But the OP said he had problems even pasting a copy of the project to a point after the existing material ended, and that the pasted material was out of sync, whereas the problem with Slide Over affected only the downstream material getting moved out of the way. So I think there' still something going on here that's not going to get fixed by Ripple Editing unless I misunderstood the problem description.