For anyone who might run into the same problem, I think I may have worked it out.
When uploading with QTM, the announce URL seems to be wrong. I manually added the announce URL from my profile and hey presto, my uploads are registering again. Not able to get back the 150GB I've uploaded for free though 
Morning!
My ratio sucks, So I thought, I'll upload a couple torrents to help fix it. I uploaded 2 torrents, on 60GB+ and a smaller 500mb one. Before uploading I was on 609GB uploaded.
So the 60+GB is currently at 1.645, and the 500GB one at 1.991.
I still have 609GB uploaded......
Between them they should have fixed my ratio enough get my downloads back, but I still sit at 609GB.
I sent the helpdesk a message but they haven't responsed.
Any ideas?