htaccess problem

My website is acting funky and I can’t figure out why one installation is working differently than another. I have a custom htaccess that I am using currently on my main site here it is:


IndexIgnore .htaccess */.??* *~ *# */HEADER* */README* */_vti*

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^.*$ - [S=45]
RewriteRule ^(gmail)/trackback/?$ /index.php?pagename=$1&tb=1 [QSA,L]
RewriteRule ^(gmail)/feed/(feed|rdf|rss|rss2|atom)/?$ /index.php?pagename=$1&feed=$2 [QSA,L]
RewriteRule ^(gmail)/(feed|rdf|rss|rss2|atom)/?$ /index.php?pagename=$1&feed=$2 [QSA,L]
RewriteRule ^(gmail)/page/?([0-9]{1,})/?$ /index.php?pagename=$1&paged=$2 [QSA,L]
RewriteRule ^(gmail)(/[0-9]+)?/?$ /index.php?pagename=$1&page=$2 [QSA,L]
RewriteRule ^(linux-shortcuts-and-commands)/trackback/?$ /index.php?pagename=$1&tb=1 [QSA,L]
RewriteRule ^(linux-shortcuts-and-commands)/feed/(feed|rdf|rss|rss2|atom)/?$ /index.php?pagename=$1&feed=$2 [QSA,L]
RewriteRule ^(linux-shortcuts-and-commands)/(feed|rdf|rss|rss2|atom)/?$ /index.php?pagename=$1&feed=$2 [QSA,L]
RewriteRule ^(linux-shortcuts-and-commands)/page/?([0-9]{1,})/?$ /index.php?pagename=$1&paged=$2 [QSA,L]
RewriteRule ^(linux-shortcuts-and-commands)(/[0-9]+)?/?$ /index.php?pagename=$1&page=$2 [QSA,L]
RewriteRule ^feed/(feed|rdf|rss|rss2|atom)/?$ /index.php?&feed=$1 [QSA,L]
RewriteRule ^(feed|rdf|rss|rss2|atom)/?$ /index.php?&feed=$1 [QSA,L]
RewriteRule ^page/?([0-9]{1,})/?$ /index.php?&paged=$1 [QSA,L]
RewriteRule ^comments/feed/(feed|rdf|rss|rss2|atom)/?$ /index.php?&feed=$1&withcomments=1 [QSA,L]
RewriteRule ^comments/(feed|rdf|rss|rss2|atom)/?$ /index.php?&feed=$1&withcomments=1 [QSA,L]
RewriteRule ^comments/page/?([0-9]{1,})/?$ /index.php?&paged=$1 [QSA,L]
RewriteRule ^search/(.+)/feed/(feed|rdf|rss|rss2|atom)/?$ /index.php?s=$1&feed=$2 [QSA,L]
RewriteRule ^search/(.+)/(feed|rdf|rss|rss2|atom)/?$ /index.php?s=$1&feed=$2 [QSA,L]
RewriteRule ^search/(.+)/page/?([0-9]{1,})/?$ /index.php?s=$1&paged=$2 [QSA,L]
RewriteRule ^search/(.+)/?$ /index.php?s=$1 [QSA,L]
RewriteRule ^category/(.+)/feed/(feed|rdf|rss|rss2|atom)/?$ /index.php?category_name=$1&feed=$2 [QSA,L]
RewriteRule ^category/(.+)/(feed|rdf|rss|rss2|atom)/?$ /index.php?category_name=$1&feed=$2 [QSA,L]
RewriteRule ^category/(.+)/page/?([0-9]{1,})/?$ /index.php?category_name=$1&paged=$2 [QSA,L]
RewriteRule ^category/(.+)/?$ /index.php?category_name=$1 [QSA,L]
RewriteRule ^author/([^/]+)/feed/(feed|rdf|rss|rss2|atom)/?$ /index.php?author_name=$1&feed=$2 [QSA,L]
RewriteRule ^author/([^/]+)/(feed|rdf|rss|rss2|atom)/?$ /index.php?author_name=$1&feed=$2 [QSA,L]
RewriteRule ^author/([^/]+)/page/?([0-9]{1,})/?$ /index.php?author_name=$1&paged=$2 [QSA,L]
RewriteRule ^author/([^/]+)/?$ /index.php?author_name=$1 [QSA,L]
RewriteRule ^([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/feed/(feed|rdf|rss|rss2|atom)/?$ /index.php?year=$1&monthnum=$2&day=$3&feed=$4 [QSA,L]
RewriteRule ^([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/(feed|rdf|rss|rss2|atom)/?$ /index.php?year=$1&monthnum=$2&day=$3&feed=$4 [QSA,L]
RewriteRule ^([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/page/?([0-9]{1,})/?$ /index.php?year=$1&monthnum=$2&day=$3&paged=$4 [QSA,L]
RewriteRule ^([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/?$ /index.php?year=$1&monthnum=$2&day=$3 [QSA,L]
RewriteRule ^([0-9]{4})/([0-9]{1,2})/feed/(feed|rdf|rss|rss2|atom)/?$ /index.php?year=$1&monthnum=$2&feed=$3 [QSA,L]
RewriteRule ^([0-9]{4})/([0-9]{1,2})/(feed|rdf|rss|rss2|atom)/?$ /index.php?year=$1&monthnum=$2&feed=$3 [QSA,L]
RewriteRule ^([0-9]{4})/([0-9]{1,2})/page/?([0-9]{1,})/?$ /index.php?year=$1&monthnum=$2&paged=$3 [QSA,L]
RewriteRule ^([0-9]{4})/([0-9]{1,2})/?$ /index.php?year=$1&monthnum=$2 [QSA,L]
RewriteRule ^([0-9]{4})/feed/(feed|rdf|rss|rss2|atom)/?$ /index.php?year=$1&feed=$2 [QSA,L]
RewriteRule ^([0-9]{4})/(feed|rdf|rss|rss2|atom)/?$ /index.php?year=$1&feed=$2 [QSA,L]
RewriteRule ^([0-9]{4})/page/?([0-9]{1,})/?$ /index.php?year=$1&paged=$2 [QSA,L]
RewriteRule ^([0-9]{4})/?$ /index.php?year=$1 [QSA,L]
RewriteRule ^([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/([^/]+)/trackback/?$ /index.php?year=$1&monthnum=$2&day=$3&name=$4&tb=1 [QSA,L]
RewriteRule ^([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/([^/]+)/feed/(feed|rdf|rss|rss2|atom)/?$ /index.php?year=$1&monthnum=$2&day=$3&name=$4&feed=$5 [QSA,L]
RewriteRule ^([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/([^/]+)/(feed|rdf|rss|rss2|atom)/?$ /index.php?year=$1&monthnum=$2&day=$3&name=$4&feed=$5 [QSA,L]
RewriteRule ^([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/([^/]+)/page/?([0-9]{1,})/?$ /index.php?year=$1&monthnum=$2&day=$3&name=$4&paged=$5 [QSA,L]
RewriteRule ^([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/([^/]+)(/[0-9]+)?/?$ /index.php?year=$1&monthnum=$2&day=$3&name=$4&page=$5 [QSA,L]
</IfModule>

# END WordPress

If I try to use the default one that wordpress creates when you goto /wp-admin/options-permalink.php than it stops working. Here is what that htaccess file looks like:


# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>

# END WordPress

The thing that I don’t understand is I uploaded the same theme to different wordpress install version and the default htaccess that you see above works!

The two sites are hosted on the same server just in different root folders. Using the same theme I am not sure why this problem would occur.