I had the same issue with my shopify and paypal account after switching email/paypal account to a newly created paypal account. I followed the suggestion provided above but couldn't add additional email address on my new paypal account, at the same time, I realized that the email address on my new paypal account was not verified, so I verified the email address on my new paypal account and the pending amount showed up to my new paypal account right away, and the order showed as "Paid" on shopify account too.
Hope this helps.
Thanks Andrew, that was the fix. the problem was pretty much the same, and I had to actually add my registration account email address as a receiving paypal address in my paypal account. thank you so much, that was ingenious.
I'd like to take this opportunity to invite all the community to visit my online store: alyssasbox.com
Thanks again !
Fixed! I also had the same problem, I waited a few days for it process with no luck. Similar to the other reply below about the emails. My email for PayPal that was linked to my Shopify account was not confirmed. Once I sent the confirmation email from the PayPal dashboard and confirmed in my email, the payment went through immediately, all I had to do was click refresh! I hope this helps!