The HTML5 Report Viewer's content is rendered in a DIV element. Thus when you use customized pages, you need to provide proper CSS rules to style the DIV element e.g. position it relatively to the additional elements and set its sizes.
Please use the browser's Console and check the calculated styles of elements in the viewer's DIV element. Thus you can trace the CSS rules inheritance and apply proper corrections.
If you need further help, feel free to open a support ticket and submit a demo project to check your settings.
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