Okay, I don't have Gnome, so I can't test it out. But I do have Rhythmbox (RB) and it's what I'm using to transfer playlists. When you plug in your HTC, does it show up in RB? Does it work to transfer files from RB to your HTC? What directory are you writing to?
I'm wondering if your write process is what's causing the issue. What are you using to copy the files? Can you plug it in and then, without writing any data, unplug it?