Denid boarding, I have no idea. But denied check in, yes, it happened to me.
CA denied to check me in even though I:
1) had confirmed reservation. (at least in UA's system)
2) had valid e-ticket which was issued by UA. (an award ticket)
3) came to check in counter in time.(1:15 h before departue time)
I'm currently on hold with a UA agent who has informed me that they can't issue e-tickets for CA flights: only a paper ticket will do, and it has to be issued immediately upon booking. So they booked me and told me to call Japan reservations to get the ticket issued.
So I called Japan reservations to get the paper tickets, and the agent said "I'm sorry--those aren't good dates for Air China!"
Looks like I will be using NW miles for this trip.
And possibly many more...