My engine was way noiser prior to break-in.When it was new with 6 miles on the ODO. (overall engine noise)
BTW, I would change OE "fill oil", around 500-1000 miles. replace with a quality Dino Oil like castrol GTX, then use a Synthetic(Mobil 1,
a true synthetic) after approx 5k miles at minimum. I felt that it helped overall noise.
The Break-in oil builds up alot of solubles early on with a few initial miles. Yu want to dump it sooner and not wait for first 5K miles. My firm opinion.
Using Mobil 1 is your personal call, and Dino
Castrol GTX regular oil is great stuff too.
I believe 2008+ Matrix's and most of all Toyotas are using 5w/20 oil now if I'm correct. (for better MPG and to meet MFR. Federal Cafe Laws.) I would rather have 5W30 which still meets Toyota GL-4 spec's for warranty purposes.
It has a slightly higher viscosity and runs a quieter valve train!
But the so called vacuum noise yu describe is Intake "Induction Vacuum" heard at the Air Box.
What has the dealer said??? I'm curious. Yu will probably get three different answers from 3 different people.
BTW, my Matrix engine was very, very
rough idling when new. But after break-in it became smooth as can be. (around 4-5k miles, when I started getting my best MPG@ 36 Hwy.)
Hope this makes some sense to your situation!
LT