Intranet Zones are prompting for Credentials

I have 3 Applications/Websites and they are added to Intranet Zones and Enabled Automatic logon with current user name and password through Group Policy. But still users are complaining like single sign on is not working for these sites. We have users logging through local desktops as well as through Terminal Service. Both users are facing the issue. Any assistance will be appreciated.
Anwar MAsked:
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DrAtomicCommented:
Check that the browser used is actually seeing the domains as intranet zones and not as internet. Also this article may be helpful: https://support.microsoft.com/en-us/kb/258063
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Anwar MAuthor Commented:
I have read the Article "https://support.microsoft.com/en-us/kb/258063" already but this doesn't solve the problem. And one more thing I need to noted here is only the 3 sites having problem others are working fine. We use IE11 and we have IE9 also in the environment. We don't see the issue in IE9.
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DrAtomicCommented:
I don't have IE11 here, but check to see if the option "Automatically logon local intranet zones (or whatever fits this description)" is enabled in IE11; it is enabled by default in previous IE versions but may very well have been turned off by default in IE11 as an additional security measure.
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Anwar MAuthor Commented:
Everything looks fine in IE settings, am confused because issue is only for three sites. Others are working fine. So anything needs to be done at site level.
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DrAtomicCommented:
Ok, that means further debugging then;

Try running Fiddler (http://www.telerik.com/download/fiddler) on the non working installations and compare the results with a working IE11 installation.

Also check your raw http logs for clues as well as both server and client sided eventlogs.
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