if you update by just installing newer versions over an existing copy (which is not running at the time, of course).. then your settings will remain. the ini file does not ship with the install binary and therefore will not over wright your settings

if your keyclone is not saving your settings.. and you are on vista.. then you must -always- run as administrator.

do this by setting the properties on the shortcut (shortcut/properties/advanced/always run-as admin)

let me know if that helped