We're working on this as we speak; the system should have actually removed the limits when you signed up for Prime, indicating something's gone wrong along the way. I tried overriding it myself, but cPanel's still refusing to see anything other than the 512mb.
I've got the system working on a fix-quotas check first; if Google isn't misleading me today that's one of the non-destructive ways that might fix the problem. I'll keep you posted once that finishes; it may take some time to run though, as it fixes everyone's quotas and re-scans everything as opposed to just 1 user.