Yeah. With any MFI constant flow system there are always puddles of fuel on the back of the valve when it opens. Way more than a carb’d deal.
So maybe the header was was tugging so much harder on the port it was pulling more raw fuel out the pipes. Without knowing if the A/F ratio changed or what it’s hard to say.
As sr440 said above, a good header will change cam timing requirements. His was a great example of that.