The issue here is that each axis and the series provide the data points to the tooltip, which then eliminates any duplicates. Because there are 2 different date formats it is mistakenly treating them as different values and showing both. The only way I can think to avoid it is to pre-format your date:
var parser = d3.time.format("%d/%m/%Y"),
formatter = d3.time.format("%a %e %b %Y");
data.forEach(function (d) {
d["Date"] = formatter(parser.parse(d["Date"]));
}, this);
You then need to use this new format when setting your time axis:
var x = chart.addTimeAxis("x", "Date", "%a %e %b %Y","%Y");
You still need to have this line:
x.tickFormat = "%a %e %b %Y";
This is because the x axis will still default to providing the date format as %Y. It's a bit of a pain but I think this is a bit of an unusual case. Here's an update of your fiddle:
I hope that helps
John