Remember, You must to initialize the upload library with each upload.
$this->load->library('upload');
$this->upload->initialize($config);
User guide: http://ellislab.com/codeigniter/user-guide/libraries/file_uploading.html
Edit:
You can check the $_FILES array and check if there are the name of the screenshot input and the logo input, if they aren´t, you can create the array you need
I´ve found this:
A simpler way to have create that data structure is to name your HTML file inputs different names. >If you want to upload multiple files, use:
<input type=file name=file1>
<input type=file name=file2>
<input type=file name=file3>
Each field name will be a key in the $_FILES array.
http://www.php.net/manual/es/features.file-upload.multiple.php#53933