The upload issue and the post-checkout order-processing issue are unrelated, so I'll address each one in turn here.
This help page explains some common reasons for upload problems and how to resolve them:
That said, we have noticed reports of random upload issues affecting a tiny minority of users lately and been trying to track down the reason. Unfortunately, there's no clear cause or any common factor we've been able to identify so far, but it seems to be related to upstream network issues (e.g., ISP connectivity or router hardware) rather than hardware/software issues on our users' own computers.
If possible, you might try rebooting your router (if there's no power switch, just pull the power plug, wait ~10 sec., then plug it back in), or retry the upload from another location with a different Internet connection. If that's not practical or still doesn't work, you can email our support team for an alternate method of providing file(s) for us to upload for you:
The post-checkout thank-you page you quoted above is a generic page we display to buyers when they arrive there before we have received IPN (Instant Payment Notification) from PayPal confirming their payment. PayPal can sometimes take longer to complete a payment than it takes for the buyer to finish checkout; we cannot process the order until we receive IPN from PayPal for their payment, at which time we issue download links, send emails to you and the buyer, and log the order details.
If you are having to approve payments manually in PayPal, please see this help page for instructions on having that handled automatically:
The troubleshooting instructions on this help page will walk you through sorting out other common issues that may interfere with transmission of IPNs from PayPal to our system: