EnergyPlus strange behavior with epJSON input - depends on file name?

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I am running EnergyPlus v9.4.0 on a Windows 8.1 computer from the command line and I am finding some strange behavior when using epJSON files for input.

My command is of the form: energyplus -w USA_HI_Honolulu.Intl.AP.911820_TMY3.epw -r honolulu_reference_buildings.epJSON

Sometimes the model runs successfully with no issues.

Other times, the model runs until it prints "Initializing Simulation" to the terminal and then it stops. It does not seem to actually run the simulation. It produces output files, but most of them are empty. It only has data in .shd and .eio files. The .shd file looks the same as when the model runs successfully. The .eio file is shorter: it ends at line 263 (ZoneVentilation Airflow Stats Nominal...), while the .eio file has 307 lines when it runs successfully.

It seem like whether it runs depends on the name of the epJSON file (I tried copying the file and changing the name), my working directory, and random luck.

Does anyone have any ideas what may be going on, or suggestions on how to get it to successfully run more reliably?

Some additional context: I started with a .idf file produced by BEOpt for EnergyPlus v8.8.0. I converted this to a .idf for v.9.4.0 using the IDFVersionUpdater. I then converted the .idf to a .epJSON using the -c option for the energyplus command. The model ran fine when I used the .idf file, but I would like to use the .epJSON format to facilitate automatically editing the file in another script.