if you are running JIRA 6.x, please download my pre-v3.1.2 from my server at http://www.polscheit.de/plugins/jira/gantt-chart/gantt-3.1.2-JIRA6.jar and install that JAR-file via "upload" button on JIRA's page "manage add-ons". Then open your browser's console (also see my wiki: https://polscheit.atlassian.net/wiki/x/DgBM) and switch back to Gantt-Chart. Within the console, you should see a lot of additional information, like sample below:
Please copy and paste all the console output into the body of a support request (see menu item on screenshot below: clicking on it will automatically open a standardized email) for further analysis.
Please use menu item "support request" available within the menu of the "?"-icon to write an email, which will automatically create a related issue with my JIRA. That's easier than processing this on Atlassian Answers, here.
Based on your request above: don't you see the customfield "Gantt Options" having a checkbox for milestones? If not, than contact your administration to configure the related edit- and view-screens to contain that customfield, which is not done automatically by installing the add-on (this would not make sense as you can have multiple screens depending on individual settings).
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