1. Yes, I installed .htaccess along with the rest of Q2A package.
2. From Godaddy (quoting): "Yes, you can create an .htaccess file for your aliased domain name. "
I might just found a clue:
1. I removed .htaccess on the *main* Godaddy account folder (leaving .htaccess of Q2A untouched)
2. In my site's Q2A admin I got this message:
"The installed version of PHP was compiled without multibyte string support. Searching will be less effective for non-Roman characters."
And option #2: "/index.php/questions/123/why-do-birds-sing " was disabled
Does this help?