To help you we need more information about what you try or do ...
Do you try a fresh desinstall / install ?
If you just update be sure the files are not put in a subfolder because the install add his own input when you select your root folder. The shortcut will correct to this new exe file and it can't work alone.
I have this same problem. The Loader and everything is installed, and I just used it, but in the middle of transferring some files, the light stopped blinking, and the computer said that the device was taken out. Could it be that my USB burner died?