Thinking about it, the issue could be related to the bug I reported here:
 
http://forum.cakewalk.com/Issue-when-using-Normalize-in-multiselect-m3763740.aspx
 
By default, Sonar/CbB stores multiple clips in the same file, but sometimes Sonar/CbB gets confused as to what clip is what. This is almost 100% reproducible when using Process Effect, but maybe it affects deletes in some cases too.
 
The workaround is to bounce a clip to itself before doing any edit and/or processing operations. 
 
Additionally, I usually check the "Create one file per click" box within the Save dialog to stop Cakewalk from storing clips this way in the first place.
 
[Edit] - Note that "Bounce to clips" is different from "Bounce To Track" which you mentioned earlier.

Actually I bounced to clips, I just remembered wrong again.
Thank you for interresting inputs, msmcleod!
Much appreciated.   :)

Like he said, check the take lanes.  Even if you "don't use them," stuff sometimes ends up in hidden takes and messes things up unless you are aware of it.

Like I said. There were no take lanes. :)
If I come across this again, I will find the "Apply trim" 

Moxica
Like I said. There were no take lanes. :)
If I come across this again, I will find the "Apply trim" 

rithclick-over-the clip & do apply-triming

I'm sure there is a simple way to accomplish that, however, in the interest of time and assuming you are not using take lanes, I export that one track to a program like Sound Forge.  Without changing the length or altering the track in any way except zeroing the volume of the part or parts I need zeroed.  Then port it back into Cakewalk and the issue is solved.  May not be the right way, but has worked for me for a long time.  I have also exported specific tracks that have a challenging noise problem and treated them likewise and it has gotten me through the mud quickly.  Just a thought.

Thanks! :)
I have not experienced this anymore, but now I apply trim regularly.
I solved my issue by bouncing to clip(s) and restart Cakewalk.

I had the same thing happen but nothing fixed it so I had to make a new track and deleted the old one. I call it "Ghosting".

If you have a project with this send it to us so we can analyze the issue