aegir 0.4

When Aegir writes (or re-writes) settings.php and drushrc.php, how does it figure out which install profile to reference?

Here's why I'm asking:

I just upgraded to 0.4 alpha 11 from 0.4 alpha 6 and had to re-verify all my sites to get them to come back online after the upgrade. When I "verify" a site, Aegir rewrites settings.php and drushrc.php. (That is:
/var/aegir/platforms/myplatform/sites/mysite.com/settings.php and
/var/aegir/platforms/myplatform/sites/mysite.com/drushrc.php)

On Aegir 0.4 Alpha 5, I received "Welcome Emails" from webmaster@domain.com but not with Alpha 8. Is this a know issue? Is there a work around? - Thanks!