Ken,
 
I have noticed that some upgrades and patches have made unexpected changes to my settings.  I had a similar problem to what you are seeing with one of the X2 patches.  Somehow I ended up with a project with mixed 16 bit and 24 bit audio files.  Lots of clicks and pops.  I reset my settings to convert to 24 bit on import and record bit depth and things were OK on new projects.  I had to manually convert the 16 bit tracks to get the project to play well.
 
I have also had upgrades/patches unexpectedly change my playback and record timing master which caused clicks, pops, and synch problems.
 
It is worth checking your settings after patches.  I keep a notebook with screenshots of my settings that I verify after major changes now just to be safe.
 
Glen