I used your code and modified it slightly to run a whole bunch of cylinders
with random endpoints.  I'll post my image in p.b.i for you.  If you can see
your problem with it maybe can can explain it a bit more carefully.  (BTW
the speckles on the ends of the cylinder come from the gradient having
coincident surfaces where it is repeating, multiply the scale factor by
something miniscule like 1.00001 to get rid of it)

code used:

camera {
  up y
  right x*image_width/image_height
  location <0,0,-10>
  look_at < 0,0,0>
}

light_source {
  <0,100,-10>
  color rgb <1,1,1>
}

background {color rgb 1}


#declare R1=seed(1);

#declare i = -5;
#while (i<=5)
  #declare j = -3;
  #while (j<=3)
    #declare p1 = <-1*rand(R1),-1*rand(R1),-1*rand(R1)>*5*(rand(R1)-0.5);
    #declare p2 = <1*rand(R1),1*rand(R1),1*rand(R1)>*5*(rand(R1)-0.5);
    cylinder{
      p1, p2, 0.2
      texture{
        pigment{
          gradient (p2-p1)
          color_map{
             [0.0 color rgb <1, 0, 0>]
             [1.0 color rgb <0, 0, 1>]
          }
        }
        scale vlength(p2-p1)
        translate p1
        finish {
          ambient 0.8
          diffuse 0.5
          specular 0.1
          roughness 0.01
        }
      }
      translate x*i+y*j
    }
    #declare j=j+1;
  #end
  #declare i=i+1;
#end


-tgq

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