Hello Pamplemousse, I had the exact same infuriating issue today in fact.

I had contacted two supervisors at the beginning of the week and needed references from both of them.
Only one got back to me- not my director of studies.
I had to e-mail the funding body to advise that the second reference will follow. I sent off the application late this afternoon because I had put a lot of work into it and there were at least 5 other documents which I had written to accompany the application.

My other potential reference (director of studies) didn't even reply to my e-mail....:-S...they still haven't replied...If and when they do, I'll forward on the reference. I have no other choice as a distance learning PhD student.
I hope this works :-S. Let us know how you got on.