I posted a reply a few days ago but it's somehow disappeared
Anyways, your "issue" is that you have the option "Adjust fretboard area so all notes show" checked. This is on the 2nd page of the Scale Generator, below the root note/position boxes. If your fretboard is already set the the appropriate number of frets you want then you don't need to check it.
This option will add padding to the start and end - so when the start is the 1st fret then it obviously can't go any lower! But if you were starting at the 5th you'd get a blank fret below also.
Perhaps adding a checkbox here with a drop-down might make it explicit:
[X] pad left/right with [1/2/3] frets
Getting rid of the checkbox and having [0/1/2/3] in the drop-down would be nicer. I'll raise a ticket for this!