We can't reproduce that behaviour here, can you create a reproduceable case? At a minimum we will need to see the configuration of the Zip Files step you are using (you can copy the step to the clipboard then paste to an email or a forum post, an xml fragment for the step will be pasted). But a reproduceable case (build file and folder that doesn't zip correctly) would be much better...
Is there anything unusual/invalid about the folder and/or file names being zipped?
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