I have added an addon domain to my account, nothing to do with Q2A. Thing is the code in htaccess is redirecting my addon domain and I think it has something to do with the rewrites. Here's my htaccess code.
DirectoryIndex index.php
<IfModule mod_rewrite.c>
RewriteEngine On
# redirect any domain other than www.domain.com to www.domain.com
RewriteCond %{HTTP_HOST} !^www\.domain\.com$ [NC]
# force https on www.domain.com
RewriteCond %{HTTPS} ^off
#RewriteBase /
RewriteCond %{REQUEST_URI} ^(.*)//(.*)$
RewriteRule . %1/%2 [R=301,L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^.*$ index.php?qa-rewrite=$0&%{QUERY_STRING} [L]
</IfModule>