What drive model? What firmware? Check the Plextor site for the latest version and flash the drive. Most drives in the last couple of years have the self test feature. Check your manual or the manual posted on the Plextor site to see if your drive has that feature and how to run it.
The application checks the interface, inquiry string, drive features and write/read. All the functions that explorer should. If the application works, you may have a system issue.
Try the drive on another PC to see if you still have the same problems from the desktop. If the problem follows the drive, its the drive. If it works, its your system.