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When creating a new version with the Create New Version Tool in ArcMap, multiple versions with similar version names are not distinguishable from the pull-down menu on the New Version dialog box.
The versions in the drop down list are presented in the order of the workspaces present in ArcMap's Table of Contents.
An alternative solution is to create the new version using the Version Manager dialog. The command uses the first workspace in ArcMap's Table of Contents. If required, move the order of the workspaces in the TOC for the Version Manager to open the correct geodatabase.