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A few things to try, but it sounds like you went through a lot already
1) Was the user previously able to connect to a database (or is it a new thing)
2) What recent updates were performed (server or client side) that could possibly conflict. IE Java is a popular suspect amongst OSX problems.
3) What are your other, functioning, users connecting with (OS, hardware), any suspect differences?
4) Can you update to 10.7 or 10.8 to see if that works?
It sounds like there is an incorrect saved userID/password for that Filemaker server in the user's keychain. Go into the Keychain Access application while logged in as that user (I think it's in the /Applications/Utilities folder in 10.6). Search for "Filemaker" and delete any keychain entries you find.
When you reconnect to the server with Filemaker Pro, it should prompt you for credentials.
... one of the downsides of keychain...
Good 'thinking outside the box' George.
yeah, I'm not primarily a mac user ironically since we develop in PC at work (mac at home though). Didn't even think of looking in the keychain, as we don't normally train users to save their passwords in any way.
Thanks for the tip George!
Just a follow up on the problem ...
There was nothing in the keychain to cause the problem (not sure how that would have prevented files from being displayed).
As far as I can tell the laptop was in pretty much in sync with other machines in the office so there shouldn't have been any differences. Since they are there for staff to use while traveling it's not very clear if there was a previous problem with this machine or not.
Anyway, wiping the drive and restoring from an image solved the problem and it's working fine. Of course, I hate to give up without figuring out where the problem was, but it took far less time to re-image the laptop than I spent troubleshooting the problem already.