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This is now fixed in current master branch and as well as 2.0 dev version. Please get latest from the GitHub Chartjs repo and check the tooltip sample files.
The issue was the tooltips getting generated used relative positioning dynamically. The code sample is updated to use proper positioning for both relative and absolute positioned elements.
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This appears to be an issue with chart.js. 2.0 is coming out soon, so I will wait for that.
Source:stackexchange.com