Exceptionally frustrating. I have just found that two course I attempted to upload were saved to Garmin>NewFiles under a different name,when I move them to the 'courses' folder, it works. A pain in the arse, but a work around until it's fixed properly.
The file being sent to your Garmin is NOT a FIT or GPX file. Clearly a web site issue. They have a sticky message that says they know about the problem and is looking into it.