Earlier today I moved my blog from a site subfolder to its own subdomain to get the .htaccess file to work in a root folder, so that I could enable permalinks on a GoDaddy Deluxe shared hosting server. I did a clean install of the latest WordPress version in a newly created subdomain folder, then uploaded my plugins and themes and imported my data. Upon enabling permalinks on the subdomain, everything took and my permalinks are now working perfectly... well, almost.
I did discover one rather bizarre issue that arose as a result of enabling the permalinks that hours of researching has failed to resolve. My blog is one section of a larger site that uses javascript menu navigation. I was using this menu without any issues on my blog when using WordPress' default URL structure, after adding the script to the index.php file. However, once permalinks are enabled, it appears that the only page on the blog that can find the menu is the entry page. Clicking on any of the categories, archives, tags or post links causes the menu to disappear. I added the menu script to the pages.php file just in case, but it didn't help.
Here is my old installation, still set to the default URL structure, in which the menu works in all areas of the blog.
http://acailawendesigns.com/wordpress/
And, here is the new subdomain install with permalinks enabled, in which the menu only shows on the first page of the blog.
http://thebuzz.acailawendesigns.com/
Any ideas on how to correct this so that the menu displays across all areas of my blog on the new subdomain installation with permalinks enabled (as it does on the old blog install with the default URL structure) would be greatly appreciated.