I understand now. I was being somewhat facetious with the "antivirus?" suggestion anyway - that is prescribed as a possible culprit far top often in my opinion.
I personally am not experiencing a "jerky" analyzer. That said, if I enable the checkbox for "high resolution" in the upper right of the analyzer window, the display is not as super-smooth, but I would not describe it as jerky either.
If you still happen to have MC's auto backups from before your recent rebuild, you could try restoring just the settings from a time where you think it was still operating correctly. I have suggested this approach to many users for a myriad of "I never had this problem until I updated to the latest MC" type problems, and the success rate has been 100% to date. That said, I have no idea what setting might affect the analyzer specifically… Some of the buffering settings maybe?
Either way, it is a fairly simple and painless to restore settings from old backups, and you never know, one of them just might do the trick.