Interesting, I haven't seen that before. FWIW, running java -jar /usr/local/ibmiaccess/acsbundle.jar /PLUGIN=cfg /LIST does return the systems for the current user. Is your script running as the same user or a different one?
You should be able to see which acsbundle.jar is being used in the macOS app by selecting the help > About menu option.
To see which configuration is being used, try the Edit > Preferences menu option, then select the Local Settings tab and look at the Configuration Root value.
If the config root are not the same between the app and command line, try setting that when running from the command line (see the com.ibm.iaccess.AcsBaseDirectory property in the getting started guide sect. 9.3)
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Carl G
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