Well, I had similar problems, was trying to book a flight last week from YYZ-YZF on AC for YYZ-YEG and 7F from YEG-YZF. The plus was that having another airline in their dropped the fees by $30... but with the booking fee it doesn't change much! (At least there's a free meal on 7F)

The agent I was talking to and trying to work with to get the routing (as no 7F flights appear on AE's site) went on a long rant about it being a labour fee since they are doing the booking and that they aren't slaves. Also informed me that the web site isn't supposed to be a complete booking tool just to save a bit of time for some bookings and that it makes complete sense that not everything is bookable online.

Anyway, suffice it to say I ended the conversation fairly quickly at that point..anyway, I'm going to try again later this week and see if I have better luck.