I believe I have a work around. It appears that the OS X is sad when the keychain isn't instantly available to use when you login. I'm guessing the PHD sync process is locking the keychains folder/files when the keychain program is trying to use them. My work around is to create a symlink to a hidden folder in /Users/ for each user to store their keychain. I did this with the network home folder redirection setup included with work group manager. I followed the process here: http://houseofmac.wordpress.com/2010/11/03/os-x-network-home-folder-redirection/ but created a folder called .Keys in /Users/ and configured the mcx settings like this: Everyone needs to have write permissions to the .Keys folder. I tested with the temp folder as described in the initial directions, but the temp file is emptied at reboot which will cause the keychain message to re-appear (once) at login. Now the first time a user logs in to the machine, they will receive a message about the keychain, but it will only happen once. It's not perfect, but way better that being prompted multiple times.
Have a good day,
Chuck