Hi Adam,
Are you opening the file of choice by double clicking on it from your desktop or a directory?
If so, remember that JMP keeps a running list of your most recently used files in the home window.
Open JMP and then select the file or journal you want to work with from that list and your should only get the that file of choice to open and not a new home window along with it.
If you have been doing that already and get a new home window everytime you open a file then contact JMP support at support@jmp.com and let them know what you are experiencing.
HTH