I have used AC e-tickets extensively, but not since the system merge. The FF number should appear directly beneath the passenger name. I've never used my C+ number with an AC ticket, so perhaps this is normal. I would definitely ensure that the FF# is printed on your BP (but I'm sure you know to do this!).
I've just looked at some of my old e-ticket receipts and several of them don't show seats. I definitely did have reserved seats. There was never a problem with this.
I have a theory that there's a room full of people sitting at typewriters somewhere in Winnipeg creating these receipts and manually feeding them into fax machines. Naturally, they occasionally make mistakes. This would also explain why it takes so long for AC to get them to us.