This is a revival of issue 1298962 (http://bugs.python.org/issue1298962) from 2009. I can reproduce the problem with an MSI created by cx_Freeze and bdist_msi on a Windows 7 64bit system in a company domain. Python is at version 3.6.0, cx_Freeze is at 5.0.1. I am a user with elevated user rights but not an admin. When installing the MSI, the files are always copied to C:\, whether I have changed the installation directory in GUI or stuck to the default path 'C:\Program Files (x86)\foo'. The program is executable and runs fine. The Uninstaller removes all files without a trace.

Following the suggestions from issue 1298962 I have modified the MSI tables in Orca by adding a new Property entry with key 'SecureCustomProperties' and value 'TARGETDIR' fixes the MSI. It now installs into the desired directory. I can reproduce this on multiple builds.