Yes !!! That did the trick!!!
I changed the code to

open FILE, "c:\sample.java";
while(<FILE>)
{
  s/\r/\n/g;
  print "$_\n";
}
close FILE;
[download]

And it printed the file correctly.

thanks for your help. I was so puzzled. How did you figure it out?

regards,
Abhishek.