For starters, don't use prototypes unless required. In other words, drop the () on the sub line.

It would probably be better to pass the file name as a parameter.

You should localize your file handle.

I see that @lines is not declared either. I don't see any reason for this to be a global. This is probably the reason you're seeing the wrong config file.

sub read_the_config {
   my ($file) = @_;
   my @lines;
   local *CFG;
   open(CFG, "<$file") || log_error("Problem reading $file - $!");
   while (<CFG>) {
   ...
   return \@lines;
}
[download]

In newer version of Perl (don't know which exactly, but <updated>at least since 5.6.1</updated>), you can get rid of the local completely:

sub read_the_config {
   my ($file) = @_;
   my @lines;
   my $cfg_fh;
   open($cfg_fh, "<$file") || log_error("Problem reading $file - $!");
   while (<$cfg_fh>) {
   ...
   return \@lines;
}
[download]