I kinow this has been around a while, but my 08 5 speed has had the extra brake vac pump added but still has hard brakes on cold start sometimes. I noticed recently the pedal is occationally hard BEFORE starting which leads me to think there is a leak on the booster or check valve.
However, I also noticed the engine has very low vacuum while idling on a cold start too, its like 3-5" vac until driven a bit then it is 16-18". Anyone else notice low vac readings on cold start idle. or is it just mine?

 

if you have the SS the vac will be low at initial startup because the turbo is slightly pressurized for cold start..after about a min vac will drop to 19+,,normal ops they all do this....Hard brakes before startup? Yes, some believe thats what drove the vac pump mod because the booster is not holding pressure due to check valve design or whatever. if the pump is not working then you will observe the original problem. Maybe the pump isnt coming on all the time at start up. Otherwise everything you said is normal for those cars without the pump.(though there are some who have never experienced this,)