Joomla strips out the <br />
I believe it may also strip html entities based on what you're experiencing. One way to go around it is to double encode the HTML entities.
So & would become &amp;
Thus when it is stripped, it becomes &
You can do it with a quick search and replace of your code. (most text editors allow search and replace. With notepad i think it is Ctr+H)
Search for "&" and replace with "&"
The other method, is to create a PHP file and upload it to your server. Then use an include in mod_php.
include('/path/to/your/file.php');