Yes, I also found this symptom.
I believe that new version Setup and MGC Configurator must automatically manage these situations.
Switching between EE version, MGC Configurator should change between S.U. versions.
Now I have EE2007.3 without S.U. because I've installed EE2007.5.
There is a workaround to keeP SU with EE 2007.3. By editing the SU startup entry in the scripts.ini file under WDIR , it is possilble to use SU with 2007.3 and disable it with 2007.5.
SU is a freeware (Maybe come from Mentor Janpan) ,it may be out of sync. with formal EE release.