You can't rely on checking $! unless do contains undef. From the docs:

If "do" cannot read the file, it returns undef and sets $! to the error. If "do" can read the file but cannot compile it, it returns undef and sets an error message in $@. If the file is successfully compiled, "do" returns the value of the last expression evaluated.

Otherwise $! can contain just random garbage, which is probably what you're running into.

Update: To reply to your update, sawoy, perl is probably reading the file just fine, but because $! contains gibberish and you are exiting if it is nonzero, you are exiting anyways. Try using this instead:

#!/usr/bin/perl

use strict;
use warnings;

use vars qw($a);

my $file = 'conf.conf';
do $file
  or die "Can't load $file: $!\n";

print "a is $a\n";

exit 0;
[download]

That works for me.

Note, though, that you need to ensure that $file ends with something true (not undef, 0, or the empty string). If you use this instead:

defined(do $file)
  or die "Can't load $file: $!\n";
[download]

you will only have to make sure it doesn't end with something that evaluates to undef, but there's way I know of to tell the difference between an error and the file simply ending with undef.