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I wish I could help you, but I can't reproduce your problem.
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I'm glad to say EpubCheck is working just fine through Sigil, now. I have no idea what changed…
I actually went to run another plugin, but the cursor missed and hit EpubCheck. Wouldn't you know it, it worked! I can't figure it. I had just about given up hope, when even after verifying the environment variables path, and even stating the Java path in the plugin, it still wouldn't work. I have no idea what has changed since yesterday when it was definitely not working.
Well, it works! I'm happy. I could have made do with EpubCheck through Calibre and command line, but it's more convenient when I'm already in Sigil.
Thanks for your help.