Checked in at YYZ today using the kiosk and out come the usual boarding pass except that it's yellow (Just imagine someone using a highlighter to colour the entire boarding pass, seems like that's what they did!). Asked the agent the reason for it and they said that so they can tell who checked in using the kiosk.

Not sure the reason behind it, maybe it is used to alert agents that one will be honest and include the appropiate upgrade certificate/flight coupon?