Latest WordPress version. I did not (and do not) have this problem with WordPress 2.2 on the same server.
On /wp-admin/upload.php, there is no reference to upload.php in any link on the page.
Incorrect behavior (what I am seeing):
<a href="https://domain/wp-admin/?action=edit&ID=13">
Correct behavior:
<a href="https://domain/wp-admin/upload.php?action=edit&ID=13">