Eric,
No, I'm talking about unzipping your downloaded app.
Generally I use Zipeg for unzipping, but occasionally it runs into problems. (it appears to work but the unzipped app doesn't work. If I unzip using stuffit (the same download) it works and of course vice-versa. (The inbuilt Archive utility doesn't always work for some files which is why I have stuffit and zipeg too)
Once the app is correctly unzipped, it works fine, just like the command line tools. This problem isn't unique to your zipped file, it occurs with a number. I've just learned over the years that archiving/de-archiving packages are not all equal.
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