Stencil creation works off the dark and light points in your image. Where the image is bright the stencil will be solid and where it's dark the stencil will be transparent. It's possible that this is the case here, but without seeing one of the images causing it I can't be certain.
If this happens, you can try inverting the stencil, which switches the solid and transparent parts. If you right click the stencil and select Invert it should change.
If I've misunderstood the problem orthat doesn't fix it, could you post one of the images that does this when you convert it to a stencil here and I'll see if I can work it out.