Are try to isolate the second page in it's own file (delete all others pages).
Note that I have never used PDFs in a merge.
But assuming it does pull in the first page, you could always open each PDF and drag the 2nd page (or whatever page) to the first page position and save it then do the merge.
There is a Script «PlaceMultipagePDF» that shows how it can be done.
Dani (from Switzerland)