Well, I know that's not an argument, but I can't help but think that there always will be things that I don't know about how CIC works and/or spends their money, so it'll always be not enough data to make any reasonable assumptions. And since we don't have enough data, the probability of us just accidentally getting such good agreement in our math as the one you presented seems low for me.
As for the transparency that the refugees enjoy - it's a very political situation, I think, since it was the promise of the newly-elected government, not to mention the resonance the topic has in the world. So I see this transparency as an exception, not a rule. I don't think other, non-Syrian refugees have it too, do they?
As for the numbers: why do you only count FSW? Other economic immigrants paid the same CAD550 fee. As per the document you gave the link to, total economic immigrants target is 172k, plus 63k of dependants (that's the lower estimation). That makes it about 130mil So where does the excess go? I guess it *could* mean the economic immigrans have been paying for the refugees, and maybe some other things, all this time
Also, correct me if I'm misunderstanding it, but there under the budget figures it says that the 15-16 years budget is that high because of the fee refunds they're doing after terminating old applications. So we're paying for that, too.
And finally - I really don't know much about how government works, but CIC is not a business. I mean, I don't think they keep the fees they collect. I believe they send them to the country's budget, and from there get a smaller share as per their planned expenses. The rest might go to funding the free language courses and other newcomers services that Canada offers, for example, or who knows what else.