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Adding to what @hroderick-thr has wonderfully explained, Alteryx Designer by default packages the base workflow along with its dependencies (in this case a copy of your input file) at the time of publish to the Gallery. It does so to ensure the base workflow has access to all its dependencies (e.g. macros and input files) to be able to successfully run on the Gallery. This in-turn puts the onus on the developer/artisans to parameterize the input files.
This is the reason why your workflow runs fine the first time, but throws incorrect results in subsequent runs.
Follow the steps @hroderick-thr has mentioned and it should address your issue. Please mark his response as solution accepted if it was satisfactory and addresses your question.