I was toying with this and came up with a solution for your test script. It seems that if you do the open (read-write) '+<' instead of '<' , your second script works as intended. I just happened to see it mentioned in some docs about POSIX rules to make non-blocking pipe opens.

#!/usr/bin/perl
use warnings;
use strict;
use Glib qw/TRUE FALSE/;

my $file_pipe = "$$".'_pipe';

system('mkfifo',$file_pipe)==0 or die $!;
my $p_read;
open $p_read,'+<',$file_pipe or die $!;  # needs '+<' instead of '<' t
+o be nonblocking

$SIG{USR1} = \&on_usr1;

my $loop = Glib::MainLoop->new( 'default', FALSE );

#test non-blocking is working
my $count = 1;
print "$count\n";
#my $timer  = Glib::Timeout->add (1000, \&timer_callback, undef, 1 );

$loop->run;

sub on_usr1 {
    my $sig = shift;
    print "somebody told me $sig\n";
}

sub timer_callback{
     $count++;
     print "$count\n";
    return 1;
}
[download]

$ ./signal-w-pipe & 1 16594 $ 1 kill -s USR1 16594 somebody told me USR1