This has happened to me in the past also. It is even more fun when you upgrade filers and option become hidden in the later versions of DoT. I think partners can access a list but they are hidden from customers so that we do not play with the system and kill it. I have asked in the past for access but they are "hidden for a reason".
One way to make the hidden options show is to set them to the same value as the default..just setting the value (if 65536 for example) to the current value should make it show. To see all options you can run 'priv set advanced; registry walk options.'
Brendon I agree it is pretty silly, especially with the innocuous options I gave as examples. Really no reason to have them hidden, just impedes work and hides features - especially when I can plainly type "priv set diag" and start setting system flags. Ah well.