I've been bangin my head to the wall with this for several hours...
This problem only seems to affect IE and Edge. Tested also with Firefox, Chrome, Opera and Safari, every one of thse work perfectly.
Right after confirming purchase IE and Edge browsers are redirect to empty cart. I dumped all the event that take plase after confirming the purchase and I do see checkout_onepage_controller_success_action being used, but soon after that there is controller_action_predispatch_checkout_cart_index.
Hmm, I just noticed that with IE (and Edge) controller_action_predispatch_checkout_onepage_success and controller_action_postdispatch_checkout_onepage_success are being used twise with one go, but checkout_onepage_controller_success_action only appears between first predispatch and postdispatch.
With other browsers this does not happen. I'm thinking Magento somehow interprets one click of the confirmation button as two clicks.