I can't explain this bug, but empty space isn't a problem for emulator, so I think it s a good idea to modify the official script with your modif, to prevent this strange bug.
Can you make a try with this one,pls, it will be the next script.
;Parsing
Local $count = StringInStr($CmdLineRaw, ".exe", 0 , 1, 1)
local $app = StringLeft ( $CmdLineRaw, $count + 4 )
local $command = StringTrimLeft( $CmdLineRaw, $count + 4 )
if not $command then exit 0
hotkeyset("{esc}", "sendKey")
run('"' & $app & '"')
WinwaitActive("Project Tempest")
send("!f")
send("{enter}")
WinwaitActive("Open ROM File")
send($command & ' ', 1)
send("{enter}")
WinwaitActive("Project Tempest")
; Start the game (F2).
send("{F2}")
While WinExists("Project Tempest")
Sleep (500)
Wend
exit 0
; Stop the game - F3.
; Close Project Tempest.
Func sendKey()
Send ("{F3}")
WinClose("Project Tempest")
exit
Endfunc