I called rgb2n on $clr and then it worked.

Hm. That is weird. And I mean re-ally weird!.

$clr is (already) a number in the range 0 .. 2**24: my $clr = 2**24 / $step;, where $step interates from 10 .. 1.

rgb2n() expects input of 3 numbers in the range 0 .. 255, which it then converts to a number in the range 0 .. 2**24. So, besides the crapload of warning that should have been issued, half the lines on the graph would have been drawn in black on black:

c:\test>p1
[0] Perl> sub rgb2n { unpack 'N', pack 'CCCC', 0, @_ }
;;
[0] Perl> print rgb2n( 2**24 / $_ ) for reverse 1 .. 10;;
Character in 'C' format wrapped in pack at (eval 6) line 1, <STDIN> li
+ne 3.
10027008
Character in 'C' format wrapped in pack at (eval 6) line 1, <STDIN> li
+ne 3.
13041664
Character in 'C' format wrapped in pack at (eval 6) line 1, <STDIN> li
+ne 3.
0
Character in 'C' format wrapped in pack at (eval 6) line 1, <STDIN> li
+ne 3.
4784128
Character in 'C' format wrapped in pack at (eval 6) line 1, <STDIN> li
+ne 3.
11141120
Character in 'C' format wrapped in pack at (eval 6) line 1, <STDIN> li
+ne 3.
3342336
Character in 'C' format wrapped in pack at (eval 6) line 1, <STDIN> li
+ne 3.
0
Character in 'C' format wrapped in pack at (eval 6) line 1, <STDIN> li
+ne 3.
5570560
Character in 'C' format wrapped in pack at (eval 6) line 1, <STDIN> li
+ne 3.
0
Character in 'C' format wrapped in pack at (eval 6) line 1, <STDIN> li
+ne 3.
0
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The only possible explanation I can hazard at for this, is that you have a very (very(very)) old version of GD installed that only supports 8-bit color?

Like pre-v2.0. The libgd history doesn't list dates, but from memory, it must at least 5 years ago. I provided a patch for 2.3x, and that was at least 4 years ago.