> I need to mirror a website composed of php files. The app 
> is copying all the files but renaming them with .html 
> extension, when the original file name might be something 
> like home.php-s=0&z=1.

Yes ; because neither IE nor Mozilla will be able to open 
php files (even if they contains html data) ; only htm or 
html files will work.

> What can I do to ensure it copies 
> the files and leaves their names as they are?
Options / Spider / Check document type: Never

should do the trick!