I experienced this bug a while back. See my post on the jqPlot Google group:
https://groups.google.com/forum/?fromgroups#!searchin/jqplot-users/nickw/jqplot-users/PShgGTuXpeg/m3NPzEIWRscJ
Essentially, the code is checking to see if each line is visible before raising an event. The problem is that the visibility is not being dealt with correctly on the Javascript side (the CSS is fine), hence the issue you are seeing where a hidden series is still deemed visible.
My solution was to set s.show = s.canvas._elem.is(':hidden');
in the Series.prototype.toggleDisplay
method.
This appears to have been resolved since version 1.0.4r1120 - try updating to a more recent version to see if that helps.