Issue Between SQL and AD

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I have come across a confusing issue that I can not figure out.

We have Services Accounts in the app pools, and the correct connection strings in the Config files
We have Windows users accounts set up for the service accounts and have them in specified AD groups.
We have the same thing set up for the Windows users.
We added the AD groups to the instance and applied the appropriate permissions
But it isn't working.
So I used xp_logininfo, and I can see the Groups and members, but when I use the same thing on the users to identify Group member ship it doesn't work, unless the users are all members of an AD group that was created ages ago.
So I am at a loss here.