I don't remember this ever happening before.  I have a project with both MIDI and audio.  I added a new tempo change, actually a curve of changes, a ritard.  There's an audio clip during this section, but I don't want it to change tempo- it's a sound effect that I need played in its original form. 
 
Result:  fast series of ticking noises all during the tempo change.  Ticking stops when the ritard is over.
 
?
Randy
 
EDIT:  Solved - Altiverb caused the clicking.  Too bad!

X3e?

What happens if you up your latency time?

The clicking is probably cause by an effect that is synced to follow the tempo.  I have seen this occur often with the Sonitus Delay.  Setting the delay time manually to a fixed value has always cured the problem.
 

Check various vst plugins.
I used to get these zipper noises using Altiverb with tempo changes. 

Steve - Thanks for your reply.  Yeah, this is X3e, and changing the latency time didn't fix the problem.

Kev999 - Thank you too, you led me to the solution, And---

Carl wins the cigar.  It WAS Altiverb causing the problem.  Took the Send to the Altiverb bus out on the FX track - fixed.  You know, now I do vaguely remember a Long time ago having this problem with Altiverb during a tempo change.  

Thanks all!  Always feels good to get at least one problem solved!

Randy

Excellent. Good trouble shoot guys!

I get the same thing with certain soft synth patches, and the cure is always the same - disable any tempo based effects contained within the patch. Dim Pro & Pentagon are particularly problemesque when encountering tempo changes