how does Aegir decide what to put in settings.php and drushrc.php?

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)

With one of my sites (only one), Aegir is writing in the wrong install profile. Specifically, Aegir is doing this in settings.php:
line 20 $profile = "default";
line 50 $conf['install_profile'] = 'default';

instead of writing this in settings.php (which it did correctly for the rest of my sites):
line 20 $profile = "myprofile";
line 50 $conf['install_profile'] = 'myprofile';

And Aegir is doing this in drushrc.php:
line 21 'profiles' =>
line 22 array (
line 23 'default' =>
line 24 array (
line 25 'name' => 'default',
line 26 'filename' => '/var/aegir/platforms/myplatform/profiles/default/default.profile',

line 29 array (
line 30 'name' => 'Default',

instead of writing is this in drushrc.php (which Aegir did correctly for the rest of my sites):
line 21 'profiles' =>
line 22 array (
line 23 'myprofile' =>
line 24 array (
line 25 'name' => 'myprofile',
line 26 'filename' => '/var/aegir/platforms/myplatform/profiles/myprofile/myprofile.profile',

line 29 array (
line 30 'name' => 'My Profile',

For now, I have made corrections to settings.php and drushrc.php manually. My site works. But if I verify the site, my manual changes to settings.php and drushrc.php get blown away. This is obviously problematic for implementing upgrades--"migrating" sites--in the future.

Any insight or suggestions would be greatly appreciated. It's been a long night.

Bryan