For me it was as simple as simply not moving the cert, p12, and PP once they were created and downloaded. How stupid and unrelated is that to the error message?
Whatever, it uploaded finally.
Messy or improper /src/ folders and unintended "included" files in the package have been a long time tradition of failed apps. I think Flash Pro and a lack of strict folder conventions has always plagued people.
Once Flash Builder became the primary desirable tool for building apps, people noticed and enjoyed the simple file structure. Even still, some people from a Flash Pro-only background go back to littering the /src/ folder with things that simply don't belong there and fail apps.
I'm a native iOS developer in obj-c and am familiar with the OS itself. The word 'resources' is pretty mighty in the Apple chain. They use it to loosely refer to just about everything. It's sort of like making a folder on Windows named "My Documents". While you can (in the right spot), you can probably assume how confusing it's going to be when the user sees "My Documents" as a place to skip to in Windows Explorer, Start menu, etc but it never takes them to the folder they created. Try a synonym like 'assets' and you're typically safe, or even better, make your own folder naming convention, and keep them CLEAN.