NSERC's web USRA web page says:
Who owns the rights to intellectual property from research?
NSERC does not retain or claim any ownership of, or exploitation rights to, the intellectual property resulting from your NSERC funding. However, since NSERC's role includes promoting the use of knowledge to build a strong national economy and improving the quality of life of Canadians, every effort should be made to have the results of NSERC-funded research exploited in Canada, for the benefit of Canadians. You are encouraged to discuss intellectual property rights with all parties and organizations involved in the research.
My read: if the University decides to keep the IP, they can. In fact elsewhere, the Industrial USRA documentation explicitly gives the employing company the IP.
From what you said, I understand that your University's policy depends on if you were acting as an employee or as a student. So, what were you? Did they/will they pay you as a T4 (withheld tax) or a T4A (no withholding). If they payed you with a T4A, they were claiming you were a student, not an employee.
fwiw, I hire my USRAs as T4A
"The whole problem with the world is that fools and fanatics are always so certain of themselves, but wiser people so full of doubts." -- Bertrand Russell