on new version installation, it closes sql server management studio without asking
This fix is included in SQL Source Control v2.0, http://www.red-gate.com/MessageBoard/viewtopic.php?t=12947.
It is waiting for all copies of SSMS to close before continuing on our 64 bit Windows Server 2008 box, so that problem appears to be solved.
However, that introduces another problem: We have several developers using SSMS on a box that needs the upgrade. It would be nice if it wasn't necessary to click the Next button once all instances have exited, so a more automated install can be done. (Better yet would be to allow the components to complete installation after a reboot, similar to many MS patches. Optimal would be to allow the upgraded components to be used with each new instance of SSMS.)
This is a known issue on Windows 7. Are you using Win7 or another OS?