I'm suspecting it's a slight fault in our script that lets EP-Launch run more than one window at a time.
You can take the V6-0-0-Energy+.idd from teh Multple Transition folder, put it in the C:\EnergyPlus folder and rename it to Energy+.idd
(I'd also make a backup copy in case it happens again).
or you could reinstall EnergyPlus.
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