clicking when shifting

i have a small relay (?) box under the back seat on the driver's side that clicks when i shift from first to second gear. it'll click a couple times per shift. i've noticed that if i lessen the time that i'm on the clutch while easing the car to a start (from a dead stop) it'll click less or not at all, but if i ride the clutch a little more to make the starting process smoother then it may click 1-4 times. any suggestions/explanations for this? is it bad or what? one possibly useful note is that i have a kill switch that is hooked up in that same area. could this be causing the clicking? thanks, chris