could be related to a buggy VST. what plugins are you using? there are options to control render speed and limit it to 1x, try and limit it to that and see what happens. alternatively, disable all the plugins (ctrl-click the dot underneath the fx button on the master track), render and see if it's still glitchy.
could also be a problem with whatever you're monitoring your files back through, or possibly (but unlikely) a bad digital peaking issue on your master bus.
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