We have a bunch of bundles, organized into 5 folders. On a client, on the NAL, only one of the folder bundles show up. If the NAL is in Folder view, than all folders show, but we like the 'one-window' view. Win Explorer always shows the folders and bundles correctly. The Agent Properties show the correct associated bundles too.
I'm not sure if it is a bug or if I am missing some setting in ZCC. Most likely that later:)

Bundles are user or device associated. Win XP sp2 or sp3 clients. ZCM is on a SLES 10 sp1 box, updated to 10.1.3 (which went smoothly).