xxx.bat will not work, since the RUN command is running a process. xxx.bat is some kind of text file, not a process. The .exe files should run.
As to passing parameters, you need to understand that when you are entering a command line into the RUN filter action, you are not entering a line just like you would give on the command prompt. The commas in the RUN command are being processed by my software, not the cmd.exe program. The individual fields (which are command-delimited) are then passed into the generic Mozilla code to run a process, as an array of parameters.
I realize that is somewhat cryptic, but this command is really only intended to be used by advanced users (of which you are probably one). Just try using commas to separate parameters, even though the normal cmd.exe uses spaces for that purpose. Perhaps I should try switching to space delimited, but that will force me then to deal with quoted file names to handle the all-too-common spaces in file names, which is a bit more work.
I suggest that you test the RUN command with something simple like a text editor first.