Internal sites don’t work at Internet Explorer after Microsoft updates 10.10.2012

Microsoft released security update http://support.microsoft.com/kb/2661254/, which block using of RSA certificates that have keys that are less than 1024 bits.

You should check on other browser (Opera, Firefox, Chrome) that problem site is working. Also you should inspect which certificate has a key less 1021 bits: i may be site, Intermediate  CA or Root CA:

 

If you have that, you should change it to certificate with more strong security (2048 or 4096 bits).