If you’re on a 13th or 14th gen Intel CPU, I recommend updating your motherboard bios to the very latest bleeding-edge version, even if it’s labeled “experimental” or “alpha” by your motherboard manufacturer. I had a problem that looked just like this last year, and it turned out to be caused by the Intel voltage bug. Took me months to finally diagnose it. Updating my bios to an experimental alpha version fixed it.
If that’s not the cause, I’d say it’s likely the result of some background task occasionally interrupting everything. When that happens, Cantabile’s Profiler blames the pause on whatever plugin happened to be running when the background task intervened, just like what you’re seeing. The offending task can be hard to spot using Task Manager or other monitoring tools because it doesn’t actually consume much cpu. It merely freezes everything else as it acquires locks to critical system resources. The best way I’ve found to find the culprit is to (temporarily!) deactivate non-critical background services from the Windows Services control panel, and uninstall all non-essential software, especially anything that might try to check for updates.
–Kevin