Actually I fly CP metal and flight numbers as much as possible to avoid the problems you appear to be having. (With no status on AC, I can barely get through on the telephone to get my Aeroplan balance and update on "land transaction" postings. Their web version is quite useless in this regard, and it is hoped AC will adopt CP's almost real-time FF account retrieval system.)
My flights to YHZ are all CP numbers and metal, and booked originally in the slightly costlier ($175 return) M-class so I could use my "new" stickers. I haven't had any experience trying to book upgrades on AC metal, though I know when we were looking for award seats a few weeks ago, the CP agent had problems "communicating" with AC's computer and accessing that inventory for CP seats.
I know many of us are posting inappropriately or indiscriminately from AC to CP about the other carrier. I just assume those of us interested in these carriers will be reading both sets of forums (fora?).
And, yes, like you I also detest those "pop up windows". They are as bad as the cards which fall out of our magazines by the millions: I dub them "magazine dandruff".