They have to be checkered, that is how transparency is shown. :]
Erase everything on the layer, or just make a couple of new layers, they will be transparent automatically. Draw lines on one layer and colour on the other. :]
Please feel free to ask if you don't get it to work, I'll try my best to help. ^^;
Does your oekaki work though? Like you can draw and all? If you can't draw at all, I suggest you update your Java. :] (It's probably a good thing to do anyways.)