Thank you Bruce!
I got it to work but then it was plotting each values (imaginary and real parts of the three eigenvalues) over time. Which is interesting but not what I meant to do exactly.. I was thinking just plotting the imaginary and real parts at a given time for a given set of parameters. I rectified the code using a ListPlot instead. It seems to work except that it does not plot anything!!!! Somtimes, I get a message saying the input value lies outside the range of data and the plot remains empty. I am not really sure why it is not plotting any values.
Do you have any idea?
  Manipulate[
   Module[{soln, col1 = RGBColor[1, .47, 0], 
     col2 = ColorData["HTML", "SlateBlue"], 
     col3 = ColorData["HTML", "Black"]}, 
    ListPlot[{{Evaluate[{Re[
           eigen /. {n1 -> #[[1]][t], y -> #[[2]][t], m -> #[[3]][t], 
               b1 -> b1, a11 -> a11, f11 -> f11, f1 -> f1, h1 -> h1, 
               g11 -> g11, g1 -> g1, k1 -> k1, mm1 -> mm1, p1 -> p1, 
               p11 -> p11, d1 -> d1, e -> e, r -> r, fm11 -> fm11, 
              fm1 -> fm1, hm1 -> hm1, gm11 -> gm11, gm1 -> gm1, 
              km1 -> km1, rm -> rm} &[
           soln = Quiet@
             Benesystem[{b1, a11, f11, f1, h1, g11, g1, k1, mm1, 
               p1, p11, d1, e, r, fm11, fm1, hm1, gm11, gm1, km1, 
               rm}, {n10, m0, y0}, t]]]}][1], 
      Evaluate[{Im[
          eigen /. {n1 -> #[[1]][t], y -> #[[2]][t], m -> #[[3]][t], 
              b1 -> b1, a11 -> a11, f11 -> f11, f1 -> f1, h1 -> h1, 
              g11 -> g11, g1 -> g1, k1 -> k1, mm1 -> mm1, p1 -> p1, 
              p11 -> p11, d1 -> d1, e -> e, r -> r, fm11 -> fm11, 
              fm1 -> fm1, hm1 -> hm1, gm11 -> gm11, gm1 -> gm1, 
              km1 -> km1, rm -> rm} &[
           
           soln = Quiet@
             Benesystem[{b1, a11, f11, f1, h1, g11, g1, k1, mm1, 
               p1, p11, d1, e, r, fm11, fm1, hm1, gm11, gm1, km1, 
               rm}, {n10, m0, y0}, t]]]}][
       1]}, {Evaluate[{Re[
          eigen /. {n1 -> #[[1]][t], y -> #[[2]][t], m -> #[[3]][t], 
              b1 -> b1, a11 -> a11, f11 -> f11, f1 -> f1, h1 -> h1, 
              g11 -> g11, g1 -> g1, k1 -> k1, mm1 -> mm1, p1 -> p1, 
              p11 -> p11, d1 -> d1, e -> e, r -> r, fm11 -> fm11, 
              fm1 -> fm1, hm1 -> hm1, gm11 -> gm11, gm1 -> gm1, 
              km1 -> km1, rm -> rm} &[
           soln = Quiet@
             Benesystem[{b1, a11, f11, f1, h1, g11, g1, k1, mm1, 
               p1, p11, d1, e, r, fm11, fm1, hm1, gm11, gm1, km1, 
               rm}, {n10, m0, y0}, t]]]}][2], 
      Evaluate[{Im[
          eigen /. {n1 -> #[[1]][t], y -> #[[2]][t], m -> #[[3]][t], 
              b1 -> b1, a11 -> a11, f11 -> f11, f1 -> f1, h1 -> h1, 
              g11 -> g11, g1 -> g1, k1 -> k1, mm1 -> mm1, p1 -> p1, 
              p11 -> p11, d1 -> d1, e -> e, r -> r, fm11 -> fm11, 
              fm1 -> fm1, hm1 -> hm1, gm11 -> gm11, gm1 -> gm1, 
              km1 -> km1, rm -> rm} &[
           soln = Quiet@
             Benesystem[{b1, a11, f11, f1, h1, g11, g1, k1, mm1, 
               p1, p11, d1, e, r, fm11, fm1, hm1, gm11, gm1, km1, 
               rm}, {n10, m0, y0}, t]]]}][
       2]}, {Evaluate[{Re[
          eigen /. {n1 -> #[[1]][t], y -> #[[2]][t], m -> #[[3]][t], 
              b1 -> b1, a11 -> a11, f11 -> f11, f1 -> f1, h1 -> h1, 
              g11 -> g11, g1 -> g1, k1 -> k1, mm1 -> mm1, p1 -> p1, 
              p11 -> p11, d1 -> d1, e -> e, r -> r, fm11 -> fm11, 
              fm1 -> fm1, hm1 -> hm1, gm11 -> gm11, gm1 -> gm1, 
              km1 -> km1, rm -> rm} &[
           soln = Quiet@
             Benesystem[{b1, a11, f11, f1, h1, g11, g1, k1, mm1, 
               p1, p11, d1, e, r, fm11, fm1, hm1, gm11, gm1, km1, 
               rm}, {n10, m0, y0}, t]]]}][3], 
      Evaluate[{Im[
          eigen /. {n1 -> #[[1]][t], y -> #[[2]][t], m -> #[[3]][t], 
              b1 -> b1, a11 -> a11, f11 -> f11, f1 -> f1, h1 -> h1, 
              g11 -> g11, g1 -> g1, k1 -> k1, mm1 -> mm1, p1 -> p1, 
              p11 -> p11, d1 -> d1, e -> e, r -> r, fm11 -> fm11, 
              fm1 -> fm1, hm1 -> hm1, gm11 -> gm11, gm1 -> gm1, 
              km1 -> km1, rm -> rm} &[
           soln = Quiet@
             Benesystem[{b1, a11, f11, f1, h1, g11, g1, k1, mm1, 
               p1, p11, d1, e, r, fm11, fm1, hm1, gm11, gm1, km1, 
               rm}, {n10, m0, y0}, t]]]}][3]}}, 
    AxesLabel -> 
     TraditionalForm /@ {{Style[e1, col1], Style[e2, col2], 
        Style[e3, col3]}}, PlotRange -> All, AxesOrigin -> {0, 0}, 
    PlotStyle -> {col1, col2, col3}, ImageSize -> {500, 500}, 
    ImagePadding -> {{40, 10}, {10, 25}}]], {{b1, 1, "b1"}, 0, 2, .01, 
   ImageSize -> Tiny, Appearance -> "Labeled"}, {{a11, 1, "a11"}, 0, 
   1, .01, ImageSize -> Tiny, 
   Appearance -> "Labeled"}, {{f11, 1, "f11"}, 0, 1, .01, 
   ImageSize -> Tiny, Appearance -> "Labeled"}, {{f1, 1, "f1"}, 0, 
   1, .01, ImageSize -> Tiny, Appearance -> "Labeled"}, {{h1, 1, "h1"},
    0, 1, .01, ImageSize -> Tiny, 
   Appearance -> "Labeled"}, {{g11, 1, "g11"}, 0, 1, .01, 
   ImageSize -> Tiny, Appearance -> "Labeled"}, {{p1, 1, "p1"}, 0, 
   1, .01, ImageSize -> Tiny, 
   Appearance -> "Labeled"}, {{p11, 1, "p11"}, 0.1, 1, .01, 
   ImageSize -> Tiny, Appearance -> "Labeled"}, {{d1, 1, "d1"}, 0, 
   1, .01, ImageSize -> Tiny, Appearance -> "Labeled"}, {{g1, 1, "g1"},
    0, 1, .01, ImageSize -> Tiny, 
   Appearance -> "Labeled"}, {{k1, 1, "k1"}, 0, 1, .01, 
   ImageSize -> Tiny, Appearance -> "Labeled"}, {{mm1, 1, "mm1"}, 0, 
   1, .01, ImageSize -> Tiny, 
   Appearance -> "Labeled"}, {{fm11, 1, "fm11"}, 0, 1, .01, 
   ImageSize -> Tiny, Appearance -> "Labeled"}, {{fm1, 1, "fm1"}, 0, 
   1, .01, ImageSize -> Tiny, 
   Appearance -> "Labeled"}, {{hm1, 1, "hm1"}, 0.1, 1, .01, 
   ImageSize -> Tiny, Appearance -> "Labeled"}, {{gm1, 1, "gm1"}, 0, 
   1, .01, ImageSize -> Tiny, 
   Appearance -> "Labeled"}, {{gm11, 1, "gm11"}, 0, 1, .01, 
  ImageSize -> Tiny, Appearance -> "Labeled"}, {{km1, 1, "km1"}, 0, 
  1, .01, ImageSize -> Tiny, Appearance -> "Labeled"}, {{e, 1, "e"}, 
  0, 1, .01, ImageSize -> Tiny, 
  Appearance -> "Labeled"}, {{r, 1, "r"}, 0, 1, .01, 
  ImageSize -> Tiny, Appearance -> "Labeled"}, {{rm, 1, "rm"}, 0, 
  1, .01, ImageSize -> Tiny, 
  Appearance -> "Labeled"}, Delimiter, "initial populations", {{n10, 
   1, "species10"}, 0, 10, ImageSize -> Tiny}, {{m0, 1, "species20"}, 
  0, 10, ImageSize -> Tiny}, {{y0, 1, "species30"}, 0, 10, 
  ImageSize -> Tiny}, {{t, 1000, "maximum time"}, 1, 1000, 
  ImageSize -> Tiny}, SaveDefinitions -> True, 
 ControlPlacement -> Left]