In Simplify Profiles 6.x, setting a Profiles object to perform operation at application start/end on the Config tab results in the profile operation not applying. In all versions of 6.x, a bug prevents this option from taking effect.
All Profiles objects, both HKCU registry operations and file operations, should be configured to perform at user logon/logoff.
This issue is present in all versions of 6.x. Tricerat will address this issue in a future release. A date for release is not available at this time.