You didn't mention in your post if there had been problems prior to the installation of your new humidifier and roof vents, but at first blush it looks like another case for the old adage, *if it ain't broke, don't fix it!*
My guess is that the heating contractor recommended the humidifier, and the roofing contractor recommended the vents. The problem is that now your house is spewing LOTS of heated air out through the roof vents during the winter, and because the air that replaces it is moisture-laden (from the humidifier), you're getting condensation as soon as it hits the cold roof deck.
The irony of all this is that *conventional wisdom* says the things your contractors did are completely according to protocol and should serve to prevent such problems as you're having now. The reality, however, is that you're now having problems you didn't have before.
The term *Weatherization* has been applied to the relatively new (i.e. not universally accepted) science of heating & insulation. If you're interested, you can find lots of information at www.weatherization.com, and there are also weatherization threads at www.pathfinder.com/TOH/ ("This Old House") and www.fixerupper.com/ ("Fixer Upper").
At the very least, you should be able to have your heating contractor replace the *more efficient* humidifier with a less powerful one (at his expense). However, once you've learned more about weatherization you may find other things you'd like to have done.
P.S. A bleach solution should work for the mildew, but you don't want to be doing this every year!