When using admin.php to point to the /system folder, sometimes admins will end up redirected from urls with /admin.php to urls with /system. This presents problems with various add-ons, and generally speaking if I set everything up with /admin.ph pI'd like to keep them there. Is there an .htaccess rule I can use that will ensure that?
One thing I've noticed, which may not apply to your issue, is that if you create a Nav shortcut to a page in the EECP, and then later change the URL to your CP, those previously created Nav shortcuts will not be updated. This will cause missing pages should you click those shortcuts after the URL move.
The solution is to delete the shortcuts and recreate them. Maybe there's a way to edit them, but that's what I did to fix that particular issue.