You can only resolve that by editing the PHP code.
Most of the links that are constructed use the templates... which you've already adjusted... but some use the PHP functions to generate the links... such as the pagination and bread crumb navigation bits.
I don't recall the precise change I did to have mine working... but you can emulate what I did by simply searching all of your PHP files for "forumdisplay" and then making the judgement call as to whether you should change that instance of it.
I think you're likely to find that bit in admin/functions.php though