There are some inconsistencies with the Air Canada checkin system. Just last year I booked via Air Canada a trip of 21 flights, made of 9 non-stop and 6 pairs of connecting flights, so this happened sometimes that I could not check in through those that were connecting flights but everything was OK.
First, as you did try the AC site. When you booked through them, that is the site that is most likely to work. Be careful though because they sometimes give you more than one Reference Number (for my 21 flight trip, I had 3), so you have to use the right one at the right time. All numbers were listed on the booking confirmation.
Checkin opens about 23 hours ahead of a flight. When you have a very long flight followed by another, it is possible the next one is still more than 23 hours away, so checkin will not be available. When you have a short and a long then, you may be able to check in one way but not the other because of this.
Sometimes they just can't do it. Although this did not apply to Lufthansa on any on my segments, one AC followed by 2 GOL domestic connections forced me to check in manually at the counter in Brazil.
You mention seat selection which was even spottier throughout my itinerary. I found that doing the selection via TAP Portugal was more success than others, even for non TAP flights (at least for those corresponding the the right reference number). Also they do let you select seats that got ignored by the next airline which happened when I connected from TAP to Thai Airways. This is compounded if you have airline status as some non-AC flight could see my level - and provide the privileges that come with it - but some did not.