There is nothing wrong with your boost control system - it is doing exactly what your ECU is telling it to. That is indicated by the boost error which is minimal. Also your boost gauge is off, and you are hitting around 13 psi.
You are hitting your boost target. The only reasonable explanation is that you are running the wrong map. Or you are at very high elevation maybe?
There is an issue with knock on the high end. Could be bad gas or an issue with the map. Put a good map on and see whether it persists. If it does, it is enough that you have to take care of it right away.
Clean your MAF (find the instructions that indicate it is the hidden wire up in the tube that you gently mist with MAF cleaner) and check all the hose clamps on the intake track especially between the MAF and the turbo.
What map does the AP tell you you are running???
You should be using the 2007 sti stage I map for the appropriate gas (91 octane, 93, or AZ, Ca, NV). Make sure it is on your AP (or download it from Cobb) and follow the directions from Cobb exactly (strong battery, everything powered off). Especially do not turn off the ignition if there is any issue during the process. Run it as the base map and as the on the fly map. Note when you load a new map or reset the ECU it may take a while for your boost to come up to target (if Cobb resets your DAM at <1 which I think they do).