When you package an installation up into a *.MSI file, the MSI "database" holds the default installation location (the TARGETDIR). This uses the variable [ProgramFilesFolder] as the pointer to wherever this folder is.
The location of your program files folder is stored in the registry, but there's also other locations you need to consider before moving it, such as the Program Files\Common Files folder's location. Check out the following link for tips on how to move your Program Files folder to another drive,
http://www.jsiinc.com/SUBG/TIP3200/rh3236.htm