Here's another tip from Steve Thomas, esteemed 4.5 beta engineer. This one involves a specific error you may receive when sequencing Microsoft Visual C# 2005 Express Edition based applications:
Issue: When a virtualized Microsoft Visual C# 2005 Express Edition based application is launched for the first time, and the first time only, the following error may appear:
The automatically saved settings file 'C:\Users\<UserName>\Documents\Visual Studio 2005\Settings\C# Express\CurrentSettings.vssettings' cannot be found. You can change this file on the 'Import and Export Settings' Tools Options page. The IDE will use your most recent settings for this session
Cause: This is expected behavior when these kinds of applications are virtualized. The reason for this is because the location of the most recent settings are saved in the registry during sequencing but they are not found at first run because they exist as a generic reference to the user profile path.
Resolution: To avoid this error, remove references to the settings in HKCU\Software\Microsoft\VCSExpress\8.0\Profile during sequencing (after the first launch).
J.C. Hornbeck | Manageability Knowledge Engineer