One big difference you need to keep in mind when pasting in X3 is that clip overlaps in the same lane are strictly disallowed. Even if you have the "Blend" option selected in editing preferences,  X3 will slip edit any existing clip in the target area of the paste to prevent overlaps. One scary side effect of this is that if the paste completely covers an existing clip, that clip will get slip-edited into oblivion such that only Undo can recover it. 
 
I filed a problem report that if the Blend mode is active, a new lane should automatically be created for the pasted clip to accommodate the overlap rather than eliminating it, which should only happen in Replace mode.
 
But other than that, I haven't really had any trouble with cut/copy/paste. If you can reproduce a specific problem (and describe in such away that others can reproduce it here), you need to file a formal problem report. Just reporting on the forum that you're seeing "All kinds of weird" is not going to get anything looked at or fixed.
 
http://www.cakewalk.com/support/contact/problemreport.aspx
 
 
 
 
 

Huh... I actually came across this once!   There was a small clip that seemed to disappear when I pasted other clips in.   I figured out what happened, but I do agree it would be best to add a lane if an existing clip(s) falls entirely within the region by other clips being pasted in.   Or at least a warning to that effect.
 
But otherwise, copy and paste seems to be working OK here... though I don't really use the Delete Hole option often. 

Clint Swank
So, I select 16 bars, all tracks. Do cut special, delete hole.  Hole is not deleted. Same thing with delete special.  Tried the same thing in X2.  Works perfectly. Ideas?

Yes, this bug has been confirmed by several people, including myself.  I filed a problem report to CW last night and received confirmation that development is looking at it.
 
The workaround is easy and obvious:  After the deletion just move the material that Sonar should have moved back in time to the measure(s) where you want it.  No big deal.
 
JG
http://www.jerrygerber.com/symphony8.htm
 

For delete hole to work consistently with midi data "non-destructive midi editing" needs to be disabled in preferences.

Clint Swank
OK.  I tried a bunch of things, and stuff got even more screwed up.  There's a serious problem with all cut and paste functions with midi tracks.  Disappearing clips.  Clips cut but not pasted.
All kinds of weird.  So I opened the same tracks in X2.  Completely normal.  Fix please.

Did you submit a problem report with these steps outlined?

Filed a problem report about the initial issue, also talked to tech support who confirmed it. Didn't keep track of subsequent problems trying to find a workaround, at least not well enough to file a coherent problem report.  The workaround is to use X2 for this type of structural manipulation, since it works, and then use X3 once everything's bounced to audio, where the problem apparently doesn't exist.

Clint Swank
So, I select 16 bars, all tracks. Do cut special, delete hole.  Hole is not deleted. Same thing with delete special.  Tried the same thing in X2.  Works perfectly. Ideas?

I don't think it is a bug.  I thought it was.  Someone mentioned that in Preferences-Editing-MIDI if you uncheck "non-destructive MIDI editing" the delete hole function will work as expected.  When this box is checked, the data is not actually deleted but made invisible, therefore the data after the delete point is not moved over to the apparently empty measures.
 
JG
http://www.jerrygerber.com/symphony8.htm