I had to restart the mission, Miller never gave me any prompt for the flare/pickup, so when I went to that cliffside marker nothing was happening, I played back through, grabbed Chico but this time on the way Miller mentioned the flare, so when I had Chico instead of just a circular landing zone icon it had a mission marker, and Miller talked to me when I got there, saying put Chico down, call in the chopper etc.!
Strange glitch in such a polished game, but if it ever happens to anyone else a restart solved mine!! :D Thanks for all the responses guys, this one was just a good ol' fashioned bug!!