And again, whatever I'm going to use it for, shouldn't this be allowed in perl?

Yes, it should and is. I think everyone responding is in no doubt that the problem is something other than the front of the string magically disappearing.

Try putting this in place of the print (in the chomp-less version):

  printf "total of %d bytes read (%d including carriage returns)\n",
    length($wholeString), $. + length($wholeString);
[download]

and comparing that to the length of the input file as reported by the dir command?

I'm just printing it out in the DOS box.

I've seen console windows omit bits of the output when flooded with data. Have you tried doing ConvertFindLaw.pl PilotLifeFindLaw.htm >tempfile and looking to see what's in tempfile?