I do not know weka, but as a rule, jitter is the term for changing a periodic signal to some reference interval. I assume that the slider allows you to set some range or threshold below which data points are considered regular, or change the output to make some changes. A wikipedia entry may give you some background.
Update: from this pdf , the jitter slider is used for this purpose:
Jitter for handling nominal attributes (and for detecting "hidden" data points)
Based on the accompanying slide, it looks like it is introducing some changes in the visualization, possibly to show when two data points overlap.
Update 2: This google books compilation (for data mining by Jan Witten, Abe Frank) seems to confirm my assumption:
[jitter] - a random offset applied to the X and Y values ββto separate points lying one above the other. Without jitter, 1000 instances at the same data point look exactly the same as 1 instance
Rich seller
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