When you upload a non text file into an assignment, and later download that file, the file has two new line characters added at the beginning of the byte stream corrupting the file. I have done a lot of testing, because I thought the bug was mine. The file is uploaded correctly and somewhere after pluginfile.php branches processing depending on the activity type, and before the send_stored_file function is called the new line characters are appended. I could not find the location myself, though I tried.