Making SEO URL's Work With Two Stores

I've spent the last seven hours trying to make something work and can't figure it out. Any help would be GREATLY appreciated!

I've upgraded to 1.4.4 and am running two stores.

All SEO URL's work perfectly in Store 1.

But in store 2 when I click on a SEO URL I get this error message:

Internal Server Error
The server encountered an unrecoverable error.

This is usually caused by a faulty, or improperly installed CGI script or .htaccess file.

Here's what I have in the .htaccess (residing in my opencart directory).

Options +FollowSymlinks

RewriteEngine On
RewriteBase /opencart/
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)\?*$ index.php?_route_=$1 [L,QSA]

NOW HERE'S A CLUE: If I remove the subdirectory from line two of my .htaccess so it reads:

RewriteBase /

then the SEO URL's will suddenly work in Store 2 BUT Store 1's SEO URL's will no longer work. (In store 1 I get a message that no input file is specified.)

There has to be a way I can change the .htaccess to have fully functioning SEO URL's in both Store 1 and Store 2 at the same time.... isn't there?

Has anyone else experienced this dilemma?

Is anyone else running two stores with SEO URL's that work?

I'll gladly buy a beer (via Paypal) to the first person who can help me fix this. ;-)

I have 2 stores. 1 opencart and on old oscommerece using seo urls in a sub directory.
The correct .htaccess file is in each directory.
With the path for each one correct and it works ok