I hear what everyone is saying, and a new site is already in the making, in the mean time I have managed to fix this issue.
For reference, the includes/application_top.php includes a parameter check that will throw up a 406 error if the URL sting exceeds 43 characters. A bit short with more modern hash lengths, especially if you have some additional parameters appended to the URL.
On line 25 (in my version) of the includes/application_top.php, it shows
Code:
if (isset($_GET[$key]) && strlen($_GET[$key]) > 43) {
Change 43 to a more suitable higher number and the 406 error disappears for me.