The visual studio add-in just displays an object reference not set to an instance... message and closes, the standalone utility shows the same message, but lets you view the report which shows every reference in the .csproj as "No such assembly exists" and also every reference in the web.config file as "No infragistics assemblies were found"
This was trying to upgrade from 2008.2 -> 2009.1
Upgrading the project by hand worked fine.
I upgradraded a project ASP.NET with Infragistics 2006 vol1 to 2009 vol1 (SR). No problems. Later in the day I tried to upgrade another project (from 2007 v3 to 2009 vol1). I then got the same errors from the Upgrade Utility (even thow the upgrade program said the upgrade had been successful). I've had 2006.1, 2007.3 installed for ages (just installed 2009.1 SR today) - ready to upgrade. All work has been unertaken on the same laptop. Very odd. Don't really want to upgrade by hand (but as not reply to your POST - I doubt I've got an option).