I don't know how to trigger this, but on a partner's site we are seeing the message "Staff members are not allowed to discharge borrowers, nor borrowers to request a discharge." appear whenever the staff are trying to checkout.

I suspect the problem is here:
[% IF ( nopermission ) %]
    <div class="dialog alert">Staff members are not allowed to discharge borrowers, nor borrowers to request a discharge.</div>
[% END %]

No permission just checks the page params, but 'nopermission' is only set from trying to access discharge.pl with the 'useDischarge' syspref set to 'Don't allow'

It appears as if the 'nopermission' is getting incorrect values from somewhere