Had the same "problem" at Malaga recently...
Thomas Cook flight...."where is your reference number and print out" barked out by some English woman - I assume being a Thomas Cook Rep standing beside the check in desk while the Spanish lovely behind the desk actually continued to process the boarding card while checking my passport.
Naturally a few strong words was given to the "rep" and boarding card issued with a rather sympathetic smile from Spanish check in girl. Jobsworth Thomas Cook - and rubbish flight to!
Nivsy