I would have to agree with @ahockley since I had this exact same problem with my wordpress blog. Which is happening is that the .htaccess file is getting overwritten and then when you set it to custom and then back to default it corrects itself for a while. What I had to do was something like this:(this is the default)
# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>
# END WordPress
Change to:
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>
# BEGIN WordPress
# END WordPress
Once I moved the # BEGIN Wordpress out of the blocks the problem stopped. Hope this helps