The API quota for my project was successfully increased to 4M through the application process. This is confirmed in the details for the quota via the Google Developer consol
So Google support got back with a note saying that we'll just have to wait for the quota refresh... I can't even see any difference from the 'increased upload' capacity and the limit does seem to be 50 (roughly at least). I've asked them how long the anti-spam upload freeze actually is but I'll carry on breathing whilst I wait for that puppy.
Special thanks for help from DalmTo and halfer though.
Message from Google Support:
I have enabled "Increased upload" capacity for your channel. Please re-login to your account and check if all works fine.
We don't have any 50 videos per day limit anymore tell the truth, but we have antispam algorithms which may temporary suspend your Upload function.
This algorithm is confidential, so I can not discuss this feature in details. If you can not upload videos you should just wait I am afraid. But I hope "Increased upload" will help.