On the same project today and I decided to freeze some synths like Kontakt, FM8 etc etc etc...
Clicks and pops returned when moving transport around, and that was happening on the tracks I had just frozen (so same problem all over again).... NOT PLUGINS!
So guess what...
I did
Utilities -> Change Audio Format to 24 bit again (remember this is already 24 bit project)...
And it went away again!
WTF?
Either I'm doing something really really stupid or Sonar is...
(I do have settings in project Preferences Audio Data: Record bit depth 24, render bit depth 32, Import bit depth original, but I can't see why this would be a problem).