Well I've noticed that returning from PayPal WPS sets the order status to "payment_received" - so if you set your uc_file settings to look for that order status as the condition where the file's added to the user, that should fix it.

I don't have the issue of the cart not clearing - every time I've tested with WPS I have not had a problem. The cart clears, the order status is payment_received, and the file shows up in the Files tab.

I hope you resolve your problem!