Are the sites not loading Secure sites? (the ones w\ the yellow lock down in the status bar) This was an answer from MS for this same problem. Check the KB article first--this seems to be an issue with IE6 upgrades.
"There are many possible reasons that Internet Explorer cannot access secure web sites. Please try the following general trouble shooting steps for this problem:
Step 1: Delete temporary files, cookies, 3rd party add ins and extensions.
Step 2: Reset Internet Explorer to the default settings.
Step 3: Ensure the Internet Explorer is configured to accept cookies.
Step 4: Ensure the firewall is not configured to block this kind of connection.
Step 5: Ensure that the network connection is not configured to block this access.
Step 6: Check if the Cipher Strength Length is 128 bit. If your Cipher Strength length is 0 bit, please refer to the following Microsoft Knowledge Base article:
Q261328 Cipher Strength Appears as 0-Bit in Internet Explorer
http://support.microsoft.com/default.aspx?scid= kb;EN-US;Q261328
Step 7: Delete the registry key below:
HKEY_LOCAL_MACHINE\System\CurrentControlSet\C ontrol\SecurityProviders\Schannel"
Hope this helps!
