Ooh, I see what's wrong. I think you _expect_ to have "us altgr-intl" and "bg phonetic". However, in gdm (the login manager) you selected "us alt-intl" instead of "us altgr-intl" (which can be seen in ~/.dmrc in the Layout= line). An explicit selection in gdm adds the new layout unless it was already configured.
So all you need to do is to fix the layout in the login manager once.
Ooh, I see what's wrong. I think you _expect_ to have "us altgr-intl" and "bg phonetic". However, in gdm (the login manager) you selected "us alt-intl" instead of "us altgr-intl" (which can be seen in ~/.dmrc in the Layout= line). An explicit selection in gdm adds the new layout unless it was already configured.
So all you need to do is to fix the layout in the login manager once.