• Try toggling the PDC button. 
• As a test, press "E" to turn all your effects off. Play your project. Does anything go "out of sync" then?

It might help if you post more about your system at this point. 

Cactus Music
It might help if you post more about your system at this point. 

Or even just more?

Thanks everyone for your concern and you help. Here's my system info....
HP H8-1256s
Core i5-2400 CPU 3.10 Ghz
8 GB RAM
Win 7 Home Premium SP1
NVIDIA GeForce GT 620
Echo Audiofire 12
Sonar Platinum (This happens in both 32 bit & 64 bit versions)
(This also happened for me in X3 Producer but NOT in Sonar 8)
As soon as I have time, I'll try some experiments with removing certain plug ins to see if I might be able to pin it down to one (or more) certain plug ins.
 

On my system, if I insert or delete any plugins whilst in play mode, it mostly causes a SONAR freeze.  Now, while a song is playing, I can adjust parameters in my plugins....
 
Is the OP saying that he can't adjust settings in his VSTs while song is playing?
 
Jim

You will need to specify exactly how you are doing this.
are you using vst2 or vst3 plugins etc. When a plugin is deleted during playback and the there is delay in the circuit, we insert a placeholder pass thru behind the scenes to manage the delay.
When bypassing the plugin is similar unless the plugin supports soft bypass. In the latter case it is up to the plugin to handle delay when bypassed.

Please submit a small repro project file.

Seems to happen in VST2 and VST3. Also, it appears that it's only happening in the Pro Channel. Adding or removing a module causes all timing sync to fall apart. I thought it might have something to do with Drumagog but, I have tried turning Drumagog off and projects with no Drumagog and it still does it.