Joomla to WordPress url problems

I have recently replaced my Joomla1.5x site with a WordPress2.6.2 blob which was built in the subdirectory. I setup the WordPress to use Permalinks

%category%%postname%

and all worked fine. I took long time over the migration(subdirectory > main-directory) and all worked well, operational within 1/2 hour of the move. I have anticipated using the .htaccess with 301 redirects to redirect a lot of old Joomla urls.
The problem that I encountered was that all the old urls instead of giving 404 errors are all redirected to the home page? i.e.
http://www.acme.biz/index.php?/web-links/resources/index.php goes directly to http://www.acme.biz/ but still shows the original url in the IE link window?
I have been reading where I can but really can’t get a handle on it. I does seem to come down to the permalink addition to the .htaccess file which if I remove completely makes the blog unavailable.

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

I’m really just a middling amateur so the in-depth coding passes over my head mostly but I’d appreciate any ideas to pursue as I’m now right out.