Well, the bulk of the cost of our PR applications are taxpayers' money, probably. As truesmile says, our $1040 probably won't even cover a week's wages for one person working at CIC. I guess they set the fee at around $1000 so that they don't get random people applying on the off chance they get approved, and so that people would take it as a serious undertaking and prepare accordingly. They won't charge us for the actual cost of processing because that could make it prohibitively expensive for people who aren't well off. It would be awful if they made people pay the full price of the costs before they issue COPR - imagine they said "your application took xxx hours to process, please pay 15,000CAD and we will issue your COPR." A lot of people who applied Inland were complaining that they paid for it so they have a right to have their applications processed within the timeframe they expected when they applied. While I totally agree that there needs to be more transparency, the argument "we paid for it" doesn't really apply. As hefty a sum as $1040 is, it's probably a small amount compared to CIC's operational costs. :/
I suppose the background checks take a long time because it has to be done outside CIC, they have to contact the respective governments and agencies, etc. Wish they didn't have to double check us, but I suppose, if someone were desperate enough to feign a genuine loving relationship to gain PR, they might also submit falsified documents or omit to mention issues that would get them denied... I don't like it any more than you do, but I can see that they can't give us the benefit of the doubt and have to put us through all the screening. Unfortunate, but it's a fact.
By the way, when did you send those 3 "additional proofs" and when did you get the GCMS notes? I know that they take a while to open their mail and attach things to your file... maybe they still hadn't gotten around to it? Or if it's been more than a few months, maybe they do take that long to go through the mail :/ Or do they (sometimes) discard things they didn't ask for? Discouraging.