It might well be Acoustic Resonance in an Open Cylinder - see wikipedia article...
http://en.wikipedia.org/wiki/Acoustic_resonance
When the boiler is on, a fan will be blowing the exhaust gasses through the flue - certain wind speeds across the face of the flue opening may be turning your new chimney into a musical instrument - like a didgeridoo.
If you can fit some kind of wind-baffle some distance from the flue outlet, so as not to interrupt the gasses coming out but to divert the wind's airflow away from the flue's opening the change may stop the resonance.
Wait until it happens again and get out there with a square of stiff board - see if you can make the noise stop by diverting the wind a little bit but don't cover the flue.
Peccavi
August 2009