Thank you for the examples and verbose problem description.
I've pushed the fix to the master that should resolve this
https://github.com/jsreport/jsreport/commit/25374beb2628340b20cc8d0207bec89103a059a6
Some low level details:
The problem is that chrome puts to the pdf a big white rectangle at the beginning.
If we want the merge to work, we need to remove this rectangle so the header can be visible.
To determine if we want to remove this rectangle, we were using its size.
There was a calculation checking if its size was bigger than the page, so it is likely the one we should remove.
This doesn't work in your example because the rectangle is smaller because of the margins.
I've changed the algorithm determining the rectangle is chrome default background and hope this will work better.