Do you have the "Your Virgin Media order" email from VM, that shows a summary of the order from their side, including the discount. MSE have a similar arrangement where its a discount on the VM side order, not by third party cashback? Also, the other clue is what your estimated first bill was showing, in the email "Your Virgin Media Contract", that would have calculated the charge for the first 2 months fees, less the "credit".
Edit: Does your "eContract.pdf" document show the credit under "Other items & charges"
Good luck, hopefully the forum team can resolve this if you have these VM emails.