The issue you are encountering is that the first element of @gl_thread_queue_arr is still a reference to the same object you are now modifying. If you want to create a new ffmpeg job, you need to create a new ffmpeg object to reference it. Something like this (built off the FFmpeg::Command example, untested):

use FFmpeg::Command;

my @gl_thread_queue_arr = ();
while (<DATA>) {
    my @options = split;
    my $ffmpeg = FFmpeg::Command->new('/usr/local/bin/ffmpeg');

    $ffmpeg->input_options({
        file => $options[0],
    });

    # Set timeout
    $ffmpeg->timeout(300);

    # Convert a video file into iPod playable format.
    $ffmpeg->output_options({
        file   => $options[1],
        device => 'ipod',
    });

    push @gl_thread_queue_arr, $ffmpeg;    # Add job to Ffmpeg queue
}

foreach my $ffmpeg (@gl_thread_queue_arr) {
    my $result = $ffmpeg->exec();
    croak $ffmpeg->errstr unless $result;
}
__DATA__
input_file1 output_file1
input_file2 output_file3
input_file3 output_file2
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