The "Please wait while iTunes configures iTunes" is a repair install of iTunes. (The advertised shortcut for iTunes has checked against the installation database in the iTunes.msi to see what itunes program files, registry entries and other itunes whatnot ought to be installed on the PC, and has discovered something missing on the PC. So it's trying to replace those items.)
MSInstaller events will be being recorded in your Applications event log about those repair installs. If we're lucky, they'll tell us what item is missing that iTunes has been trying to repair.
In Windows 7, open Event Viewer by clicking the Start button, clicking Control Panel, clicking System and Security, clicking Administrative Tools, and then double-clicking Event Viewer.
Open the Windows logs folder. Open the Application log.
Look for MSInstaller events generated at the same time as the iTunes repair installs. (You may see several different MSInstaller events for each repair install.) Doubleclick on the events to see the descriptions.
Are you always getting the same descriptions for your iTunes-repair-related MSInstaller events? If so, paste a copy of the description for each typical MSInstaller into a reply here so we can have a look, please.
