Thank you for bringing this to my attention. When running FlashFXP via the command line for automation the update check should not be performed. This might be a bug.
Could you please give me some examples of the type of command lines you are using?
In addition several builds were released with the update check forced on. We use a specific compiler flag that determines if the update check uses the user defined setting or is forced on, for development test builds this flag is turned on, however we've slipped a few times and forgot to turn it off in regular releases.
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