I have an EE site that also has a wordpress blog in a subfolder off the root. I have the LG .htaccess Generator extension installed and it is working fine, but the current htaccess file needs some rule to allow it to access the wordpress blog at www.mysite.com/blog. I know this is causing the problem because I can rename the .htaccess file to something else and the wordpress blog appears. With the .htaccess file properly named it just redirects to the home page of the EE site.
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