There is nothing mojoPortal code can do to influence file system permissions. The file gets saved to disk in the context of the windows user that is the identity on the app pool whether uploaded from file manager or from the editor.
I suggest re-apply the full control permissions to the to the /Data folder and make sure you check the option to propagate the permissions to all child objects.
Do the same with the /App_Data folder, it needs the same full control there.
In IIS 7.x, click the site then double click authentication, make sure the only things enabled there are Anonymous and Forms Authentication, make sure impersonation is not enabled.
Hope that helps,
Joe