If your ISA server 2006 is having problems with any of the following, than I would suggest looking to see if you have the KB2509553 Windows Update installed.
ISA Server 2006 Issues
- Slow DNS Lookup times
- Remote desktop not working after clients connect to VPN
- VPN server is stuck on “applying settings” when logging in
- 806 GRE Firewall Errors when trying to connect to VPN
- RRAS service crashes on ISA Server
- New clients cannot connect, VPN server entering deadlock mode
Here is the support article documenting that KB2509553 does indeed break ISA. http://support.microsoft.com/kb/2669182
You can visit the page above to download the hotfix, or click the button below. This will take you to a page where you can get the hotfix emailed to you.
** Note ** We filled out the form multiple times and the hotfix URL they emailed us was broken. Probably because this is an older issue. To resolve your problem simply uninstall the KB2509553 update on your ISA server and don’t re-install it.
Here is a technet post with people that have experience the same issue. http://social.technet.microsoft.com/Forums/en-US/Forefrontedgegeneral/thread/2fd8f0ce-83ad-4070-a5bc-36b862f4648c/
Here is a link for additional error troubleshooting for ISA Server 2006.