FWIW, I never add latency inducing effects to my project until I know I will never take them out.
SONAR is incredibly weak at managing the PDC once you actually start using the PDC. Pulling a latency inducing effect out of your project makes the timing of the project fragile and prone to manifestations such as you have observed.
If I think I want to temporarily experiment with latency inducing plugin that I will want to remove after the trial I use a special alternate version of the project file.
I do this so that I do not corrupt and screw up a project that is important. Once the project gets the kack from bad latency management it is hard to get the kack to go away.
I always either wait till I am definitely going to use the plugin or I try it on an alternate safety project.
On occasions I have seen that people have advised raising the MIDI latency buffer to make audio gremlins like this disappear or at least only appear when you project is using up lots of resources.
I just avoid the problem by never pulling a PDC managed plug in out of a project.
Timing stability is one of the things I wish Cakewalk was working on instead of what ever it is trying to work on at the moment.
Good luck.
best regards,
mike