Do you run this cgi script using the same user as when you decrypting with gpg? What happens if you run it without cgi, something like this (not tested!):

use Crypt::OpenPGP;
use File::Slurp;

my $pgp = Crypt::OpenPGP->new(Compat => 'GnuPG');
my $phrase=read_file('file.txt');

my ($plaintext,$valid,$sig)=$pgp->decrypt(
    Data => $phrase,
    Passphrase => "abc123!",
);
print "[message: $plaintext<br>valid: $valid<br>signature: $sig<br>err
+or: ".$pgp->errstr."]<br><br>\n";
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