I have an application that I have built a .msi installer for throgh Microsoft Visual Studio 2010. I recently made some updates, including changing the version number and rebuilt the installer with these updates. The installer includes shortcuts on both the desktop and in the Start menu. Running the installer appears to work fine, and both of these shortcuts work. After restarting my computer I've found that the shortcuts are changed to have a Target type of Application (Installs on first use) and the Start In: field is changed to a location that doesn't exist. Once this happens, every time you use that shortcut it tries to install the application again and fails.

I have also changed the name of the shortcut that the installer creates. This appears to work, and the shortcut still works after a restart. After the restart, though, the shortcut with the old name that doesn't work also appears on the desktop and in the Start menu.

Does anyone have any ideas what I may have set up wrong, or what I need to change to get the shortcuts to be have properly?