Installed latest update.
When I stop the recording after doing takes in loop mode, say in the middle of take 5, all the previous clips are split at that point.
 

 
The clips shouldn't be split at all...I don't think?
This is a new project, with just one acoustic guitar track.  Was going to try out the Melodyne in comping mode but can't get that far.  My first attempt at this crashed Sonar while trying to figure out this issue.  Frightened.
 
WORKAROUNDS - As explicated by a few users below, there are two reasonable workarounds:
1. Bounce each take to a clip (good if you have only a few takes)
2. Highlight and delete one entire vertical section of clips. 
    Then drag the remaining column split ends all the way left or right ( good if you have lots of takes)

like this?
http://forum.cakewalk.com/Comping-issue-with-latest-update-201706-Someone-please-confirm-m3625013.aspx

No.  I can't even get that far.  When the recording ends the above is what I get.  Split comps all at the same spot.  The last take is always highlighted, and the greyed out takes stay that way.  Each lane contains two clips instead of one.  I rolled back to May and have the same issue.  I'm thinking my registry is messed up. 

There is nothing wrong with your machine. This is how the take lanes work. The most recent take is made active and all previous takes are muted. The split happens in order to mute the overlapping previous takes.

Ah ok.  That helps.

Check out the recording modes for more info on Comp Mode vs. Sound on Sound vs. Overwrite, plus Auto Punch thrown in for good luck.
https://www.cakewalk.com/Documentation?product=SONAR&language=3&help=Recording.10.html
 

After recording you can select all the clip;s in each take lane and bounce them to clips, once per lane, thus restoring singularity of each take. I believe the new comping thing where they use previous take lanes when there are available spaces is not desirable for everyone and should be made able to turn off.

Also sometimes when I've had this happen, I've selected one portion of the split sections and deleted them, then selected all the remaining portions and drug (slip edited) them out to their original length. It goes fast.

Ah ha 6F!  Very good tip!  This eliminates that tiny split leftover space that is left behind if you simply drag the split all the way left or right.  That leftover was so weird.  I kept zooming in on it and dragging it further to the beginning or end of the take and it wouldn't go away.  I got it down to a fraction of a single sample, and realized I was wasting my time...