The reference picture's display is only available in the image-based color mode so yes when you go back to free color you can't see it. This tool is only meant to pick those colors. Maybe what you'd like to do is more importing a layer and do things manually? This is planned to be added soon.
If you're interested in making only lines, maybe this trick could help : http://forum.bleank.com/viewtopic.php?f=8&t=101
. You can then use the preseve transparency option to change their color.