I'm pretty much on the same boat as you. I subscribed via the Developer App and money is deducted from the account. On the Developer app now it says "Enrollment through the Apple Developer app is not avallable for this Apple ID" and the button is greyed out/disabled. I also have it listed in Subscriptions. When I log in to "developer.apple.com", I can see a button to subscribe enabled and I can go through the subscription again!. When I click on the username's drop down menu, It says "Pending". Have you found a solution to your problem?

has the issue been resolved now?