I found this thread because I was searching for a solution to the same problem. When I load geocache locations they wind up in my waypoints folder instead of the geocache folder on my Venture Cx. I imagine there are a lot of frustrated geocaching Garmin owners out there right now.
I have tried loading coordinates from https://my.garmin.com/geocaching and the data loads correctly into the geocache folder, so for now I won't be using the geocaching.com site.
Someone must have changed something on geocaching.com. If they now could only return it to the way it was ... like when it worked. I was ready to take my gps back to the store, as I was becoming convinced it was defective.