Hi mkelley --
I will document your request to be able to specify the name of the file to open. However, I can not reproduce the problem you describe of not opening ftm files.
Here are my steps.
Create a new script
batch process folder
open Marching Band.ftm
Set batch process folder to Finale 2k4b/templates/band templates
All templates in the folder are opened. It would be great to see only the Marching band template.