While we aren't quite sure what the cause is, what seems to be happening is that a critical file (such as the ciwweb.pl file) is being prevented from executing because the server thinks it is open (locked, being modified, still uploading, etc.). The typical resolution is to use an FTP program, such as Filezilla, to navigate to the server, delete the file, and re-upload.
If your admin module is working, viewing the error log should provide which file is causing the error. Otherwise, deleting the folder for the study and re-uploading everything also usually works.