I upgraded my Vault repository last night to 3.1.2. It would appear as if the way in which access is granted has changed. I primarily use group rights and I have a simple structure like
$
$\clients
$\clients\A
$\clients\B
$\clients\C
$\clients\C\somedir
where I was able to assign a group specific rights to a nested level such as ($\clients\C\somedir) without assigning any rights to its parent(s). I find that I must now assign Read to the root ($) in order for people to even gain access to the repository. This obviously results in inherited Read access to all children (in this case many of other my clients!

I have verified each users' individual rights assignments (Users Tab, [select user], Security button) and can confirm that the users only have rights granted through their respective groups.
I decided to manually handle the issue for now through "Folder Security" settings but it is rather tedious (denying read to individual folders). Additionally, the admin client will generate a .NET Unhandled Exception after hanging. I have yet to try to generate the steps to reproduce this on a reliable basis but would be willing to do so should it be news to the vault testing team.
Does anyone have any suggestions? This is the first upgrade problem I have experienced with the Vault product thus far. I assume that a "downgrade" isn't possible... although I do have backups -- it just seems messy.
Regards,
James