In the original color mode, the pattern pixel ('0' or '1') selects between one of two colors from the color table. If either color value from the color table is zero, then the backdrop color is used (i.e. the pixel is transparent). This is why the 9918A has color black as the second color (see pg. 2-17 in the 9918A data sheet), because you need a way to differentiate between transparent and a color. If you want to use sixteen *colors* without a transparent, then color zero needs to be your black and you need to set the backdrop color (via VR7) to black so that the zero-index transparent pixels show as black.
Using the palette above in post #570, just set VR7 to >x0 (the low nibble needs to be 0) and it should work as expected.