Sharepoint 2010 Permissions through AD not working

I'm running Sharepoint 2010 in a simple 1 App and 1 DB server setting. I am using AD to control access to sites. All the SP groups are Domain Local security groups which contains users, and then the security group is added to the site in SP where it will grant access.

Nothing has changed recently but I'm noticing that some of these groups are not working as they should. Our SP environment is not down, because 90% of the groups that grant permissions in AD for SP are working but there is 10% which seems to not be. I can't fathom why this is but if I add a user to one of these groups, then nothing happens. If i add the same user to one of the working groups, permissions work fine.

The change is nearly instant from when I add a user to a working group to when it takes affect. Even then, I looked around and find this which kind of gets near the issue. http://sergeluca.wordpress.com/2013/07/06/sharepoint-2013-use-ag-groups-yes-butdont-forget-the-security-token-caching-logontokencacheexpirationwindow-and-windowstokenlifetime/ talks about cache timeouts and such so I did the commands to lower the cache timeout to 10min instead of 10hrs; still did not work.

I don't see any errors in logs, I don't get any errors for authentication and I've done user synch successfully.

Can anyone please give me some leads that I can look at which could explain this wacky issue I'm seeing?

Thanks
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wanderingwifiAsked:
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Justin SmithSr. System EngineerCommented:
Are we dealing with multiple domains?  If so, give me the specifics.  How many domain controllers are in your environment?
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wanderingwifiAuthor Commented:
This is on our primary domain (DomainA). Server and users all use DomainA but here is also DomainB, where all workstations are. DomainA and DomainB have bi-directional trust.
There are 4 DCs for DomainA.
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Justin SmithSr. System EngineerCommented:
Ok.  So the first troubleshooting step would be to confirm replication is happening successfully to every DC.  If group membership changes aren't making their way to the DC that SharePoint is connected to, you will have authZ issues.
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wanderingwifiAuthor Commented:
Hi Ach1lles, I know that part is working because replication is 15mins and I've waited several hours with no luck.
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Justin SmithSr. System EngineerCommented:
I understand replication is 15 minutes, but have you confirmed there aren't replication errors?
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wanderingwifiAuthor Commented:
I can confirm that replication is working properly. The dcdiag passed all the DCs on DomainA.
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wanderingwifiAuthor Commented:
Ok I'm not sure what's up but I deleted the security groups and recreated them. It seems some of these security groups were corrupt or something odd. The recreated groups worked as expected.

Thanks for trying Ach1lles. Is that from Ender's series? :)
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wanderingwifiAuthor Commented:
Did not find out why it happened but recreating groups worked.
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