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During scanning some extensions put their payloads in it, but those requests are still marked as "Extender" tool. There is no "Extender" option in "Select in-scope tools" menu, and because of that token extraction (and insertion) stops work with requests issued by extensions. That leads to requests fails, that can be discovered only in the middle of the scan.
I hope it should fix this problem, but I can't test my changes. Hope you do so, before accept pull request.