That sounds like the tuner hasnt got a clue what he is doing IMHO!

What emissions test is it failing? Cause if its just on CO, then it should be a doddle to sort.

Id not expect it to take any reasonable tuner longer than about 10 minutes to tweak the idle settings to get it through an emissions test.

Even the most basic of ECU's racetech do:
http://www.racetechdev.co.uk/em36_spec.php

Still has lambda control, what more do they need?