I am having the same problem with PayPal Standard on 2.2.
I don't offer downloaded files, instead we have products that are shipped. A file 2X file download is really the same as if I shipped 2 of an item if a customer only paid once. I have been experiencing this since late last month and have been trying to fix it with a bunch of different CA configurations, with mixed results. The best i can get is no email and no stock decrement, or 2 times each.
One solution that I saw suggested but haven't tried is with the Convert Configuration option, as I never had a 1.x UC. It shouldn't be necessary if this was a fresh UC 2 install and never had to move from workflow-ng to conditional actions, could it do any harm?
Even setting all the predicates back to their defaults doesn't prevent it.
Hopefully as more people report problems the issue will get some more attention and we can get this fixed. I've read a lot of PayPal issue topics in the forums and it seems this was a problem awhile back and is still plaguing a bunch of people in different scenarios.