Please, control the "Absolute path of the media files directory" setting. You can find it at the general settings page of podPress.
Is it right? I mean: is it the one you have set before the updates?
Was it empty and is it still empty?
Does this path point to the same directory as the "URL of the media files directory"?
Are these 2 blogs parts of a WP Multisite blog? Or are these 2 blogs on the same server?
It seems that all shows should be in "johnstokes.info/wp-content/uploads/" but you are right. The last shows seem to be not there.
For instance "johnstokes.info/wp-content/uploads/js0030811.mp3".
Are you sure that this file is in that folder?
Does it have the right permissions?
The permissions for the files should be 644. if the permissions are not right it is possible that it appears as they are not in place ("Page not found").
If they are not in this folder or if the permissions are wrong then the file size detection does also not work.
That the shows not appear in the iTunes Store is related to this too.