I suffer from this issue too on Dapper. My native language is Greek. I use two layouts en_US and el_GR and switch bettween them with ctrl+alt+shift.
I have selected en_US layout as the default layout and clicked the "separate group for each window".
This way when I start an application it's window uses the default layout.
Unfortunatelly I realized that the window shown when an app needs my password to get root priviledges (eg. /usr/bin/sudo -H -S -p GNOME_SUDO_PASS -u root -- /usr/bin/update-manager) , do not follow this rule (they do not switch to the default layout when they appear at the screen).
I think this happens because when sudo window start, the focus is not taken from the previously focused window. This results in xlock and sudo using the layout selected for that window and not the default.
This issue is very very annoying for users that use more than one layout (and all non English speakers) and thus I think it should be take a highter priority.
I think the most appropriate sollution to this is to make sudo take the focus from the previously focused window and thus switch to the default layout.
An other approximation would be to show a message under or next to the password input box that would indicate the current layout.
A similar issue is faced on the password dialog that appears after locking the screen (xlock) (see bug #49222 - https://launchpad.net/distros/ubuntu/+source/gnome-screensaver/+bug/49222/ -).