Suppose there are these files.

.
./logger.conf
./test.log
./main.pl
./subdir
./subdir/Foo.pm
./subdir/Bar.pm
./subdir/Baz.pm
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logger.conf is like this.

############################################################
# A simple root logger with a Log::Log4perl::Appender::File
# file appender in Perl.
############################################################
#log4perl.rootLogger=ERROR, LOGFILE
log4perl.rootLogger=DEBUG, LOGFILE

log4perl.appender.LOGFILE=Log::Log4perl::Appender::File
log4perl.appender.LOGFILE.filename=test.log
log4perl.appender.LOGFILE.mode=append

log4perl.appender.LOGFILE.layout=PatternLayout
log4perl.appender.LOGFILE.layout.ConversionPattern=[%r] %F %L %c - %m%
+n
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And Foo/Bar/Baz.pm are the same file

package subdir::Foo;
sub test{
        print "#inc=@INC#";
        my $log = Log::Log4perl->get_logger("MyMain");

        $log->debug("Here is a debug message in ". __PACKAGE__ );
}
1;
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And I couldn't have idea of what your main.pl looks like. May be your main.pl will not be like this... I wonder if you show what it is like, you will get more clue or hints.

use strict;
use warnings;
use Gtk2 -init;

MyMain::test();
{
package MyMain;

sub test{
        use Log::Log4perl;
        Log::Log4perl::init_and_watch( 'logger.conf', 30 );
        my $logger = Log::Log4perl->get_logger;

        # Run main loop.
        $logger->debug("before gtk");
        my $win = Gtk2::Window->new;
        my $b1= Gtk2::Button->new("test 1");
        $b1->signal_connect(clicked => sub{
                use subdir::Foo;
                subdir::Foo::test();

                use subdir::Bar;
                subdir::Bar::test();

                use subdir::Baz;
                subdir::Baz::test();

                my $log = Log::Log4perl->get_logger("MyMain");
                $log->debug("after get_logger in MyMain ...quit");
                Gtk2->main_quit;
        });
        $win->add ($b1);

        $win->show_all;

        #main loop
        Gtk2->main;
}
1;
}
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If you click button, you will see test.log with these messages.

[1] main.pl 18 MyMain - before gtk
[2466] subdir/Foo.pm 6 MyMain - Here is a debug message in subdir::Foo
[2466] subdir/Bar.pm 6 MyMain - Here is a debug message in subdir::Bar
[2466] subdir/Baz.pm 6 MyMain - Here is a debug message in subdir::Baz
[2467] main.pl 32 MyMain - after get_logger in MyMain ...quit
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