We are having this exact same issue, but I don't see that this was specifically resolved.
I've double checked the webhook on Stripe and it is fully functioning with "source.chargeable, charge.succeeded, charge.failed, charge.dispute.created and charge.dispute.closed" all selected and enabled. We created a new webhook with all available events selected just to be sure, with the same results.
We are using the provided endpoint URL:
https://www.<our-web-site>.com/applications/nexus/interface/gateways/stripe.php
Any help would be appreciated.