Comment 1 for bug 1122495

Just to be sure: by duplicate, do you mean duplicate the primitive? If so, the bug is likely a duplicate of Bug #1111459 "Filters editor jumps to the first primitive".
When you set a parameter on the second (duplicate) primitive, Inkscape sets the value as expected, but also jumps to the first primitive and keep the mouse click status active, and thus sets the same value in the first primitive.