I believe you, just trying to make sense of it. From experience I'm use to putting a less restrictive exhaust on my car and seeing less boost, or opening up the heads and seeing less boost. But I'm in no way calling you a liar, just trying to understand how removing a restriction after the blower creates more boost.
You just answered your own question. Just think of the restrictive intercooler as unported heads and a restrictive exhaust. With the larger intercooler there is less pressure being built in it because it can flow more volume (CFM).
Because of this the manifold will read higher pressure because of the extra volume of air that is getting to it.