Don't shoot the messenger!
The way Johnston explained it was that when Murray departed one of the first things they found out was that there was £8m outstanding on unpaid transfer fee instalments, the next was that Murray had promised Bain various amounts for which Bain held IOU's (this is separate to the bonus that was revealed in court). Johnston informed Bain that there simply was the money to settle the IOU's, Johnston agreed that they should be honoured over a period of time and Bain also agreed to that hence the 'contract' which Johnston described as a "guideline", it was not at any time a formal legal contract and both parties were aware that there was no recourse to enforce the terms.
That's as far as I can expand as that's basically all that Johnston revealed on the matter, a rather odd situation all round.