Project doesn't stay in synch with it self while playing back.?

Hi Group,
 
I've been using Sonar for a couple of years now and along with the other DAWS that I use its possible that I may have set something in the sonar preference file that is causing my project to  fall out of synch with itself while making changes to the plugins while the song is playing. Let say I have 2 kicks samples(printed) or 2 or three snare samples (printed) mixed together thru an aux track for the main level when I adjust plug ins, disable, enable them, bring new ones in on the fly (while the song is playing) etc.
some tracks will randomly fall out of synch with the timing of the song. This can happen to any of the audio tracks I have in the project. I have to stop the project and restart it (tap the space bar twice) and the tracks resynch themselves. I have Studio One V3 and I can disable, enable,  instantiate, adjust and do just about anything you can think of to a track on the fly and it doesn't skip a beat... rock solid. That's why I'm thinking it must be a setting in the preference file.... it's probably something ridiculously simple..
 
Any thoughts? Anyone run across this before 
 
Regards
Craig

There's nothing really super cpu intensive  about the projects I'm doing these days.
 
I have the latest update to sonar plat
saffire pro 40 focusrite drivers , Mackie Control Mackie Xt and an I7 950 with 16gb ram.... ssds etc.
 
I've noticed in this update that when I jump to markers there's usually some crackling noises before the track starts playing. I've fooled with the buffer settings in the settings (default was set to 1000ms) and no matter what setting
the noises are still there. The transport response in the last 3 updates seems to have gotten more slugish for me.
In comparison Studio One V3 is very responsive. (not trying to schill for  S1 .... Just using it as a comparison)