In device manager - uninstall all your existing USB devices Then, under USB root - uninstal your USB Controller. Reboot and allow windows to re-add the controller from scratch. Then plug in all your devices.
If this doesn't solve the problem, double check that your root USB controller is using the proper driver. Check your motherboad manufacturer for an updated driver if available.
If this still does not solve the issue, your likely looking at a damaged controller (if I understood you in saying the issue is not just with the external HDD). If it is the controller - you will end up having to replace the MB in the long term to truly fix the issue.
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Good Hunting!
Captain Haplo
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