Thank you again Rona
They did an original assessment taking the contributions into account, and then a second one again taking them into account, then a third using just our Gross Pay.
This resulted in a drop of student finance entitlement of £700.
They just tell me to contact HMRC if I have a problem with amount they are using, even though I have explained I agree with the HMRC's figures.
I appreciate you can only advice on Student Finance England, I just wanted confirmation I was right before I take it further.