If fly on Rapidair regularly and seldom experience the problems you state but it does seem that people who fly out of Toronto are experiencing a higher degree of problems than others.
If we just want to be anecdotal, a CP check-in agent was quite rude to me last week, didn't bother to check the boarding pass (Executive Class) when giving me a boarding pass for an earlier flight (meaning he had to go back to the computer and get me another boarding pass) and even though I handed my Super Elite card to him (he said he didn't need it), failed to enter my frequent flier number. When I pointed this out (politely), he said brusquely "we are very busy trying to board this flight, you write down your ff number on the boarding pass stub and I will enter it later". In fact, it was about 5:45 for a 6 AM departure flight, all other passengers had boarded and there wasn't another soul around.
I will not attribute this bad service to CP only to a "rogue" agent who may not be a morning person.