Users assigned directly to a SharePoint group can access a site if a user is in a security group that is a member of the SharePoint group, it doesn't work

I recently installed SharePoint 2013 SP1 and thus far all seems to be going well. I do have one issue concerning permissions to a team site I have created:
1. If  add a user User1 only to a SharePoint group that has edit permissions to the site, that user can log in successfully.
2. If  add a user User1 only to a security group that is a member of the aforementioned SharePoint group, the  user gets "the site has not been shared with you. The security group is a global SG, though I tried changing it to universal 
but that did not help
 I have tried updating the SPSecurityTokenServiceConfig  as briefly described at this link:
http://macaalay.com/2014/05/27/active-directory-groups-and-access-denied-in-sharepoint-2013/.  I performed the steps and it did not work. I also
tried rebooting the server after that, and that did not work either.  any thoughts?
Thanks in advance for your help

Hi,
I tested the issue on SharePoint server 2013 without sp installed. It worked and I used global security group. I will test the issue on SharePoint 2013 sp1 later, and please provide more information to narrow down the issue.
Please go to site settings > site permissions > check permission, type in domain\user1, and post the result here.
If the user has been granted permission, please try logging on another machine to test if Windows credential casues the issue.
Did the issue occur to one site collection? Please test on other sites or web applications?
Please create new user to test the issue again.
Regards,
Rebecca Tu
TechNet Community Support

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