Try this....
if(isset($_FILES['zipfile'])) 
{
    $filename = $_FILES['zipfile']['name'];
    $source = $_FILES['zipfile']['tmp_name'];
    $type = $_FILES['zipfile']['type'];
    /*$name = explode('.zip', $filename); # $name[0] returns the name of the file. $name[1] returns the extension (zip)
    ; */ # Where the file will be saved. I.E. 'extracted/myFile-02151985/'
    $target = PHYSICAL_PATH."upload/";
    // Ensures that the correct file type was chosen.
    $accepted_types = array('application/zip', 'application/x-zip-compressed', 'multipart/x-zip', 'application/x-compressed');
    foreach($accepted_types as $mime_type)
    {
        if($mime_type == $type)
        {
            $okay = true;
            break;
        } 
    }
    $okay = strtolower($name[1]) == 'zip' ? true : false;
    if(!$okay) 
    {
        $msg="Please choose a zip file, dummy!";
    }
    $saved_file_location = $target.$filename;
    if(move_uploaded_file($source, $target . $filename))
    {
        global $target;
        global $unique_folder;
        $zip = new ZipArchive();
            $x = $zip->open($saved_file_location);
            if ($x === true) 
            {
                $folder=$zip->extractTo($target);
                for ( $i=0; $i < $zip->numFiles; $i++ ) 
                { 
                    echo $entry = $zip->getNameIndex($i); 
                    $filename=explode('/',$entry);
                    print_r($filename);
                    if($filename[1] != '')
                    { 
                        $filename_folder=$filename[0];
                        $filename = $filename[1]; //
                        $name = explode('.zip', $filename_folder); # $name[0] returns the name of the file. $name[1] returns the extension (zip)
                        //echo 'sfkdf'.$name[0];
                        $target = PHYSICAL_PATH."upload/";
                        $sql = "select `id` from `tracks` order by `id` desc";
                            $list = mysql_query($sql);
                            $list_num = mysql_num_rows($list);
                            if($list_num > 0)
                            {
                            $res = mysql_fetch_array($list);
                            $new_id=$res['id'];
                            } else {
                            $new_id=1;
                            }
                        $check_for_jpg = strpos($filename, '.mp3');
                        if ($check_for_jpg === false ){
                            echo 'Check file format.';
                            $source=$target . $name[0].'/'.$filename;
                            unlink($source);
                        } else {
                            $srch = array(' ','--','"','!','@','#','$','%','^','&','*','(',')','_','+','{','}','|',':','"','<','>','?','[',']','\\',';',"'",',','/','*','+','~','`','=');
                            $rep = array('_','_','_','_','_','_','_','_','_','_','_','_','_','_','_','_','_','_','_','_','_','_','_','_','_');
                            $name_song[$i]= str_replace($srch,$rep,$filename);
                            $title_name=explode('.',$filename);
                            $new_id=$new_id+1;
                            $new_filename=$new_id.'-'.$name_song[$i];
                            mysql_query("insert into `tracks` set track='".addslashes(stripslashes($new_filename))."',title='".addslashes(stripslashes($title_name[0]))."',tape_id='".$id_last."',addDate=NOW(),status=1 ");
                            $source=$target . $name[0].'/'.$filename; $target_move=$target.$new_filename;
                            if(rename($source,$target_move)) { unlink($source); } else { echo 'not';}
                            echo 'folder zip';
                            echo '<li>' . $new_filename . '</li>';
                        }
                        rmdir($target . $name[0]);
                    }
                    else { echo $target = PHYSICAL_PATH."upload/";
                        $sql = "select `id` from `test_table` order by `id` desc";
                        $list = mysql_query($sql);
                        $list_num = mysql_num_rows($list);
                        if($list_num > 0) {
                        //and, instead of using "while":
                        $res = mysql_fetch_array($list); // will return the highest "id" number
                        echo $new_id=$res['id'];
                        } else {
                        $new_id=1;
                        }
                        $check_for_jpg = strpos($entry, '.mp3');
                        if ($check_for_jpg === false ){
                            echo 'Check file format.';
                            $source=$target .$entry;
                            unlink($source);
                        } else {
                            $srch = array(' ','--','"','!','@','#','$','%','^','&','*','(',')','_','+','{','}','|',':','"','<','>','?','[',']','\\',';',"'",',','/','*','+','~','`','=');
                            $rep = array('_','_','_','_','_','_','_','_','_','_','_','_','_','_','_','_','_','_','_','_','_','_','_','_','_');
                            $name_song[$i]= str_replace($srch,$rep,$entry);
                            $title_name=explode('.',$entry);
                            $new_id=$new_id+1;
                            $new_filename=$new_id.'-'.$name_song[$i];
                            mysql_query("insert into `tracks` set track='".addslashes(stripslashes($new_filename))."',title='".addslashes(stripslashes($title_name[0]))."',tape_id='".$id_last."',status=1 ");
                            $source=$target .$entry; $target_move=$target.$new_filename;
                            if(rename($source,$target_move)) { unlink($source); } else { echo 'not';}
                            echo 'only zip';
                            echo '<li>' . $new_filename . '</li>';
                        }
                    }
                }
                $zip->close();
                unlink($saved_file_location); #deletes the zip file. We no longer need it.
            } else {
                die("There was a problem. Please try again!");
            }
    } else {
        $msg="There was a problem";
    }
}