In version 6.0.5 this still works, But as of 6.06 and 6.07 if you change a midi shortcut of a clip to "This Clip" rather than from "By Position" or any other option, the shortcut disappears and will not retain the mapping.
On a side note, Do you think under the Default tab in the app preferences, you could add a default mapping type? 99% of the time I always choose "This Clip, Layer, or Group" rather than by position. Having to change this on everything I map eats up a lot of time.
Thanks guys.