sub-directory redirect problem

I have a multi-site drupal + multisite embedded gallery2 install. Everything has been working great until I decided to change my drupal multisite install to a sub-directory install vs a sub-domain type install.

I think this has to be related to the redirect rules because when I turn off the gallery2 clean url mod everything works fine. I have only a very vague understanding of how the redirect is working and got it working the first time by simply following the instructions =) I hope someone can help me out with this one.

the installation is colorgenetics.info/feline/gallery and colorgenetics.info/canine/gallery With the standalone gallery2 installs at colorgenetics.info/feline_gallery and colorgenetics.info/canine_gallery

the redirect rules are as follows to get the drupal install to work in the sub-directory this was necessary.
just for the feline site
Code:

RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_URI} ^/feline/(.*)$
RewriteRule ^(.*)$ /feline/index.php?q=$1 [L,QSA]

for the gallery2 installation just the feline site since the others should be similar
Code:

RewriteCond %{REQUEST_FILENAME} -f [OR]
    RewriteCond %{REQUEST_FILENAME} -d [OR]
    RewriteCond %{REQUEST_FILENAME} gallery\_remote2\.php
    RewriteCond %{REQUEST_URI} !/gallery$
    RewriteRule .   -   [L]

    RewriteCond %{THE_REQUEST} /d/([0-9]+)\-([0-9]+)/([^/?]+)(\?.|\ .)
    RewriteCond %{REQUEST_URI} !/gallery$
    RewriteRule .   /feline_gallery/main.php?g2_view=core.DownloadItem&g2_itemId=%1&g2_serialNumber=%2&g2_fileName=%3   [QSA,L]
    RewriteCond %{THE_REQUEST} /feline/gallery/v/([^?]+)(\?.|\ .)
    RewriteCond %{REQUEST_URI} !/gallery$
    RewriteRule .   /gallery?g2_path=%1   [QSA,L]

And the .htaccess file from the feline_gallery folder
Code:

# BEGIN Url Rewrite section
# (Automatically generated.  Do not edit this section)
<IfModule mod_rewrite.c>
    RewriteEngine On

    RewriteBase /feline_gallery/

    RewriteCond %{REQUEST_FILENAME} -f [OR]
    RewriteCond %{REQUEST_FILENAME} -d [OR]
    RewriteCond %{REQUEST_FILENAME} gallery\_remote2\.php
    RewriteCond %{REQUEST_URI} !/feline_gallery/main\.php$
    RewriteRule .   -   [L]

    RewriteCond %{THE_REQUEST} /feline_gallery/d/([0-9]+)\-([0-9]+)/([^/?]+)(\?.|\ .)
    RewriteCond %{REQUEST_URI} !/feline_gallery/main\.php$
    RewriteRule .   /feline_gallery/main.php?g2_view=core.DownloadItem&g2_itemId=%1&g2_serialNumber=%2&g2_fileName=%3   [QSA,L]
    RewriteCond %{THE_REQUEST} /feline_gallery/gallery/v/([^?]+)(\?.|\ .)
    RewriteCond %{REQUEST_URI} !/feline_gallery/main\.php$
    RewriteRule .   /feline_gallery/main.php?g2_path=%1   [QSA,L]
</IfModule>

# END Url Rewrite section

I have turned off the gallery2 rewrite mod but I would rather not keep it like this as that will of course break any links that are out there.

When the redirect enabled in gallery2 I can see the page at colorgenetics.info/feline/gallery but when I click on an album instead of going to the album the clean url link will show in the address bar but page that shows is the gallery home page. For example the url will show colorgenetics.info/feline/gallery/v/album but the page shown will be colorgenetics.info/feline/gallery If i try to go to a picture page directly I get a page not found error.

Thanks in advance for the help