(Just to get this out of the way first: I agree with CountZero and the previous Anonymous answerer that you should consider another way to deal with config files.)

Back up a bit. Understand that your do(), if successful, puts the last expression in $config_file into the variable $return, but you're throwing that value away in your code!

This is how I'd go about it:

First, format your config file as a single hash reference expression like this:

{
  default => {
    'BM_shutts_south_00' => 1,
    'BM_shutt_north_00' => 1, 
  },
};
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I just used your defaults above, so update as necessary.

To read the config file:

# define %Log_rooms out here, where it will remain in scope:
my %Log_rooms = (
  default => {
    'BM_shutts_south_00' => 1,
    'BM_shutt_north_00' => 1
  }
);

my $return = do $config_file;
if ($return && UNIVERSAL::isa($return, 'HASH')) {
  # we got a hash reference back, so override the defaults:
  %Log_rooms = %$return;
}
else {
  # do whatever you need to do to recover
  warn "Using default values.\n"; 
}
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