I have been successful in porting over plupload into Codeigniter, but when a user uploads a file, the filename comes out like this: _1, _2, _3, etc.

What could be causing this error?

Here is my CodeIgniter Controller:

function do_upload($fileName) {
        // Settings
            $targetDir = getcwd() . "/uploads/";
            $cleanupTargetDir = false; // Remove old files
            $maxFileAge = 60 * 60; // Temp file age in seconds
            // 5 minutes execution time
            @set_time_limit(5 * 60);
            // usleep(5000);
            // Get parameters
            $chunk = isset($_REQUEST["chunk"]) ? $_REQUEST["chunk"] : 0;
            $chunks = isset($_REQUEST["chunks"]) ? $_REQUEST["chunks"] : 0;
            // Clean the fileName for security reasons
            $fileName = preg_replace( /[^w._]+/ ,   , $fileName);
            // Create target dir
            if (!file_exists($targetDir))
                @mkdir($targetDir);
            // Remove old temp files
            if (is_dir($targetDir) && ($dir = opendir($targetDir))) {
                while (($file = readdir($dir)) !== false) {
                    $filePath = $targetDir . DIRECTORY_SEPARATOR . $file;
                    // Remove temp files if they are older than the max age
                    if (preg_match( /\.tmp$/ , $file) && (filemtime($filePath) < time() - $maxFileAge))
                        @unlink($filePath);
                }
                closedir($dir);
            } else
                die( {"jsonrpc" : "2.0", "error" : {"code": 100, "message": "Failed to open temp directory."}, "id" : "id"} );
            // Look for the content type header
            if (isset($_SERVER["HTTP_CONTENT_TYPE"]))
                $contentType = $_SERVER["HTTP_CONTENT_TYPE"];
            if (isset($_SERVER["CONTENT_TYPE"]))
                $contentType = $_SERVER["CONTENT_TYPE"];
            if (strpos($contentType, "multipart") !== false) {
                if (isset($_FILES[ file ][ tmp_name ]) && is_uploaded_file($_FILES[ file ][ tmp_name ])) {
                    // Open temp file
                    $out = fopen($targetDir . DIRECTORY_SEPARATOR . $fileName, $chunk == 0 ? "wb" : "ab");
                    if ($out) {
                        // Read binary input stream and append it to temp file
                        $in = fopen($_FILES[ file ][ tmp_name ], "rb");
                        if ($in) {
                            while ($buff = fread($in, 4096))
                                fwrite($out, $buff);
                        } else
                            die( {"jsonrpc" : "2.0", "error" : {"code": 101, "message": "Failed to open input stream."}, "id" : "id"} );
                        fclose($out);
                        unlink($_FILES[ file ][ tmp_name ]);
                    } else
                        die( {"jsonrpc" : "2.0", "error" : {"code": 102, "message": "Failed to open output stream."}, "id" : "id"} );
                } else
                    die( {"jsonrpc" : "2.0", "error" : {"code": 103, "message": "Failed to move uploaded file."}, "id" : "id"} );
            } else {
                // Open temp file
                $out = fopen($targetDir . DIRECTORY_SEPARATOR . $fileName, $chunk == 0 ? "wb" : "ab");
                if ($out) {
                    // Read binary input stream and append it to temp file
                    $in = fopen("php://input", "rb");
                    if ($in) {
                        while ($buff = fread($in, 4096))
                            fwrite($out, $buff);
                    } else
                        die( {"jsonrpc" : "2.0", "error" : {"code": 101, "message": "Failed to open input stream."}, "id" : "id"} );
                    fclose($out);
                } else
                    die( {"jsonrpc" : "2.0", "error" : {"code": 102, "message": "Failed to open output stream."}, "id" : "id"} );
            }
            // Return JSON-RPC response
            die( {"jsonrpc" : "2.0", "result" : null, "id" : "id"} );
        }

External Links:
CodeIgniter
Plupload