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[EDIT]
Just for the heck of it, I've done a complete uninstall/clean/reinstall of VLC (uninstall, delete all folders/..., clean registry), and it appears to have solved the problem. Something must've gotten garbled with an update somewhere (even though I select the clear preferences/cache and all). I guess I'll need to do a thorough clean every time for VLC.
Another thing I've noticed: The "Minimize number of threads" setting introduces repeatable glitching in these MPEG files.