Batch seems to be flaky at times. Another hack, assuming you're on Windows, is to create a batch file that you can run on the directory.
Basically a forfiles command that runs something along the lines of...
IsoDraw7.exe "%1" -macro"YourMacro"
You'd need to add some verbiage to your macro to perform a save and close IsoDraw. Also note that I haven't used this in years so you'll need to confirm the name of the executable for IsoDraw and update it as appropriate.