And what does the beginning of @infile look like? Update: you can't use @infile the way you are; you would need to say:@sections = split /\n\n/, join("", @infile);since split is expecting a scalar to split. Or slurp the whole file into a $infile and use that in the split. Or just assign to sections in the first place:

open(IN,"./$file");
{
   local $/ = "\n\n";
   chomp(@sections = <IN>);
}
close(IN);
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(See perlvar for what $/ does.)