Tim, Glad that you figured it out. Maybe we can modify the KB article or setup a BPA check for that to alert the customer.
Tonino, the config files should be updated unless you have them locked down for ready only or such. Is this still a problem?
Philf, The rollups do not update the version stored on the server object at the Active Directory and does not update a specific version number stored on the machine. It is a product limitation. You can find sever enhanced versions of the get-exchangeserver which will also check for http://blogs.flaphead.dns2go.com/archive/2007/05/09/exchange-2007-update-rollups.aspx.
Diamondas, No problems so far on the update. Rollup 5 will be released today at 10 AM on Microsoft Update as mentioned above. Rollup 4 will be offered to the computer via Microsoft Update (MU) if you do not have Rollup 4 installed and have installed Rollup 5. This is a limitation of the detection logic and I am working on addressing this. It isn't critical and it can be a little confusing. It will only happen if you are in this scenario and it will happen for about 2-3 weeks until the newer rollup is released.
Robert, The NGEN issue is still there where it can take forever. We have a prototype of the fix in test but it isn't really improving the time that I would like to see. We are still working on it.
Korbyn, For your cookie issue - do you happen to have a Windows 7 DC?
Did I miss a comment that needs to be answered? Let me know.