http://forum.cakewalk.com...op-noise-m3188659.aspx
 
there may be a bug. i never had this problem with x3.

Anderton
However, I have noticed lately that some loops - not all - will click (albeit at low levels) even if there is a fade. I have finally been able to reproduce it and am sending the project to Noel to see if there's any kind of issue.

 
Well, I need to correct myself. I re-visited the projects that had the clicks at the end of loops, which were still there, so I could zip up a file and send it to Noel. However, on a hunch I removed the loop markers in the timeline, selected the clip, then typed Shift+L to set loops from the selection - the problem went away. Everything worked as it should.
 
I should note this happened in projects where I was developing loops, so there was a lot of editing going on. I think what happened is I had snap to audio zero crossings selected, but at some point, remembered to check whether it was on and disabled it. However, I may not have updated the loop or loop markers to reflect this, so there was a disconnect between the two. Re-selecting the clip and re-establishing loop points based on that selection solved the problem.

Seeing your post in another thread made me realize you're not talking about an audio loop made from Omnisphere, but a MIDI loop playing back through Omnisphere. In this case there can be many reasons why you would hear a click. Mostly they would relate to envelope times, available polyphony, and what changes occur inside the synth when it transitions from the MIDI data at the end of the loop to the MIDI data at the beginning of the loop. 
 
(FYI for future reference, re-installing SONAR when there's a problem is very rarely needed. The reason some people recommend this is because in many cases it appears to be a solution because re-installing initializes defaults that may have been unknowingly changed, and the change in the defaults caused unexpected behavior.)