From your description, I have this too but very slightly when building boost in mainly 4th and 5th from low rpms....occasionaly I hear it in third from low revs giving it a boot full.
I also have a 3-port MAC valve, VF34/P20 with full silicone inlet. (MY06 XT 2.5L)
Prior to my Verso tune the cha cha cha sound was very very noticeable & bad, you could also feel it too low in the rev range...the car was very jerky.
When I had my car retuned (pulled out the piggy back Xede and went for a Verso) , I told Sean about it and he managed get rid of most of it....he said it had more to do with the duty cycle of the 3port....so from my understanding it can be tuned out by a good tuner.

Mine only does it for a split second and then its gone but no jerking at all......in my case it probably a bit of compressor surge cause the 2.5 seems to be able to get the turbo to produce quite a bit of boost low down in the RPM range which the engine my not be able to entirely ingest at that certain RPM point.

Who's you tuner? Have a chat to Sean @ ASG.

been there before...solution seriously is to lose the VF series turbo....otherwise turn the boost down or wear it.