I have a multiple-domain account with GoDaddy (on a windows server) where I have several WP installations, all running smooth and without a problem until now. I decided to convert my main domain (the one that holds all the rest) into a WP, and all went well apart from custom Permalinks. The moment I change the root WP Permalinks from default to custom the rest of installations stop working (giving 500 error). If I un-comment the rules on my web.config on the root the other sites work but the main stops working at level one of the navigation (I use a custom menu).
It's vital for me to be able to use custom Permalinks for SEO purposes (and to keep my job!!!)
Thanks in advance,