Hi Magnus,
We can certainly get you sorted out here. The good news is that there is very little of the circuit that is different between peak and shelf, so we should be able to narrow it down quickly.
First, I'd recommend grabbing the schematic. You can find it in the tech docs section under API. There are a few versions out there, but that one is correct for my implementation. Also if you PM me your email address, I'll get the v1.0 build docs out to you so you have some reference. It will be much easier to talk about testing if you have the board layouts in front of you.
The very first thing I would look at is to make sure that the signal is getting to the right parts of the filter board when you flip the peak/shelf switch. Inject a test tone and then of course you'll need a scope or signal probe to go looking for it. We have three places to check. You'll notice that the HF switch is a 2-pole, 2-deck switch but we are actually only using three of those.
First have a look at the A common terminal, which is on the rear deck toward the inside (the bottom as the unit would sit in a rack). That terminal should always have signal regardless of the Peak/Shelf switch position.
Next, we're looking at the B and C common terminals. B is on the other side of the rear deck and C is on the front deck right next to A (don't worry, there is a picture of this in the build guide). When the switch is in peak mode, you should see the signal on the common terminal of B. When in shelf, it should be on the common terminal of C.
Let me know what you find with that and we'll take it from there.
Brian