First, please report this issue by email to IDM support to get this wrong behavior fixed for files loaded via FTP in future versions.
On tab Command
Menu item name: JS Lint FTP File (or whatever you like)
Command line: "%Env:ProgramFiles(x86)\IDM Computer Solutions\UEStudio\tools\jsl\jsl.exe" -conf "%Env:APPDATA\IDMComp\UEStudio\jsl.default.conf" -process "%ftpl" -nologo
Working directory: (nothing)
Toolbar/bitmap icon (file path): (nothing or whatever you have extraced for example from uesres.dll)
On tab Options
Program type: DOS program
Save active file: checked (or NOT checked, whatever works better)
Save all files first: NOT checked
On tab Output
Command output: Output to list box
Show DOS box: NOT checked
Capture output: checked
Replace selected text width: No replace
%Env:ProgramFiles(x86) references value of environment variable ProgramFiles(x86). %Env:APPDATA references value of environment variable APPDATA.
"%Env:ProgramFiles(x86)\IDM Computer Solutions\UEStudio\tools\jsl\jsl.exe" can be different depending on which directory UEStudio is installed on your computer.
PS: This tip was not tested with a FTP loaded file, just with a local file using %f instead of %ftpl.