I have been installing and configuring SSRS since the initial release. I have always encountered several different caveats when upgrading to a newer version or adding a new server to a scale-out deployment. In some cases there have been consistencies, but in many these differences vary. These variances may have been attributed to the different installations and configurations. One for example is disabling loop back check. I have upgraded several SSRS 2005 instances to SSRS 2008 in the past couple of months and they were all very similar installations and configurations.
My most recent upgrade required me to make a change to the registry. I have performed this task in the past on my 2005 instances, but I had not encountered it in 2008. I do realize that this is a setting at the OS level. If you perform an upgrade and the Report Server URL is accessible, but you receive a 401 when trying to access the Report Manager URL follow the steps in Method 2 of the Solution section in this KB article.
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Patrick LeBlanc, Founder TSQLScripts.com and SQLLunch
SQL Down South