Issue with .htaccess file

I finally got the trial package of SEF Advance loaded to my site, but if I use the .htaccess file that came with it my website's links don't work (you can click on a link but it just refreshes the home page). I'm using Mambo 4.6.1 and although I can get around the administration page fine, if I click Components>SEF Advance>(any item) it just reloads the front page of the administration page.

I should note that I had some issues getting the ioncube loader to install. My site is using PHP4, but I had to use php5 to get the loader installed and as such had to change the file names for the SEF files to .php5 (same with the ioncube files). I'm not sure if that could be causing the issue but figured I'd point it out. Any advice? I'm currently using a modified version of the new .htaccess so that my site will be operational - if I use:

#RewriteCond %{REQUEST_URI} ^(/component/option,com) [NC,OR]
RewriteCond %{REQUEST_FILENAME} !\.(jpg|jpeg|gif|png|css|js|pl|txt)$
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*) index.php

the links go screwy, so I'm currently using:

#RewriteCond %{REQUEST_URI} ^(/component/option,com) [NC,OR]
RewriteCond %{REQUEST_FILENAME} !\.(jpg|jpeg|gif|png|css|js|pl|txt)$
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^content/(.*) index3.php
RewriteRule ^component/(.*) index3.php
RewriteRule ^mos/(.*) index3.php

Well, since my 5-day trial is pretty much over I guess I'm just out of luck. Oh well, I hear Mambo may make some changes to their SEF in the future anyway.