So based on this information...
If the file uploaded, and you click save, and now you see a permission error, the possible ways the code sends this error are:
1. The file was uploaded by a different user in the past 1 hour, OR
2. Your usergroup does not have permission for that File-type under Attachment Rules, OR
3. You changed the selected area, but the admin disabled permission in that area before you clicked save, OR
4. The admin reduced the maximum allowed file size before you clicked save.
For #1, if you keep trying to upload the same file over and over, maybe the 1 hour cutoff is not working. It does not care if you are trying to make a new attachment or updating an old one. Just if the file itself is the same. Did you make the edits and database changes I suggested above?
For #2, it sounds like you have ruled this out.
For #3 and #4, this is extremely rare, and would only happen 1 time, and needs two admins, or you would know that you did this.
I had the same problem as you 2 days ago, but when I made the edits I posted above, the problem went away. I can no longer reproduce the problem. So if you are still having the problem now even after making the changes, I will need access to an installation where it is still occurring in order to investigate further. I would ask you to submit a ticket here:
https://www.vaultwiki.org/members/?do=newticket