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Existing server with multiple users.

New domain user logs on and everything works as normal.

User can see own profile folder.

Admin logs on and user folder is there

User logs off

Admin logs on and user folder is gone

User logs back on. All changes that they made to profile is gone.

Deleted admin profile and then logged back on as admin.

Admin profile recreated.

Admin logs off and back on profile is still there.

Any thoughts?

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Do you have any entries in your log files related to profiles? Do you have any GPOs in place that would cause user profiles to be deleted on logoff? – Zypher Nov 16 '11 at 21:47
There is nothing in eventvwr that appears to be an issue We have a GPO that maps a home drive for the users. These users don't have that drive space. However we have user A that has a working profile and User B that was created at the same time as A but didn't log on until a week after user A. Creating new users using A or B as a template, profiles are not created for either – BoBo Nov 16 '11 at 21:50
You're not using mandatory profiles are you? Also, there are GPO's that can configure this behaviour. – Dan Nov 16 '11 at 21:51
Log the users in, and run a get the Group Policy results for that user. In particular look at anything to do with roaming profiles. – Zoredache Nov 16 '11 at 21:59
Any mention of temp or corrupt profile? – xeon Nov 17 '11 at 0:30

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