Paint Bucket not filling entire selection (CS4/5)

Hello, I'm a professional cartoonist and have worked in Photoshop since the earliest versions. Since upgrading to CS4 (and now CS5), I've been having trouble using the Paint Bucket Tool, so I'd appreciate any help here.
Here's a basic example ...
1) Imagine a single layer CMYK document.
2) Draw a closed shape using the Pencil Tool (no antialiasing!) with a color of choice.
3) Select the inside of this shape using the Magic Wand Tool (again, no antialiasing!).
4) Fill the selection with the EXACT SAME COLOR using Paint Bucket tool.
5) Deselect region.
6) Now use menu options SELECT -> COLOR RANGE ... And click on the filled region (technically, that color should be selected by default since it's your current foreground color).
7) Click OK
8) Choose a new foreground color and then Paint Bucket the selected region, BUT make sure you click on the area you filled in Step 4 ... i.e., do not click on a pixel you drew using the Pencil Tool.
In CS4 and now CS5, the Paint Bucket is not including the pencilled outline when I click fill. That is, I'm left with the original pencil outline, and the filled region in a new color.
HOWEVER ... If in Step 8, I'm lucky enough to click one of the original pencil marks, the entire color region fills as it always did in previous versions.
This has grown increasingly annoying while working with my cartoons because I use the Pencil Tool to "close" gaps in my inked lines, and then the Paint Bucket to fill. If I decide to change the color of a character's shirt, I'm left with tiny spots in the gap regions.
Help would be much appreciated!!
Thanks

Thanks for your suggestions, Charles.
Here's a better explanation as to what is happening with visual examples ...
I ink my cartoons with traditional tools, and then scan a high-res copy into Photoshop. The black ink is converted to a 2 color bitmap so that there is no anti-aliasing. This file is then converted to CMYK for coloring. The black line art becomes the bottom ("Background") layer, and I add a new layer on top for the flat colors. The flat colors layer is set to "Multiply" so that I can close tiny gaps in my lines with color, without erasing the original black lines.
Visually ...
1) Bottom layer is black outline with no antialiasing ...
2) Create new layer on top for flat colors and set to MULTIPLY. Using pencil tool (and Wacom Tablet), close the gap with red ...
3) Because layer is on multiply, you can see that the red in Step 2 is actually this shape ...
4) Magic Wand to select the area INSIDE of the now closed circle. Wand is set to "Sample All Layers" so that it selects only the area closed in by the black outline layer AND the red. Paint bucket this area with the exact same red ...
5) Once again, here is what the flat color layer actually looks like since Multiply is on ...
6) Magic wand the area outside of the circle and fill with a DIFFERENT color ...
7) Now, suppose you didn't want the circle to be red. I now select the red using Magic Wand (or Select -> Color Range menu) and click on the red. An outline appears around the ENTIRE red shape (i.e., you would assume that all of the red has been selected since it is the EXACT same color ... verified using eyedropper tool) ... However, if you click to fill with Paint Bucket, here is the result ...
8) For some reason, Photoshop is "remembering" the red originally drawn using the Pencil Tool in Step 2 as a separate region ... Even though all of the colors are on the exact same layer ...
I hope this better explains what I'm experiencing here
ANY IDEAS???

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Paint Bucket not filling entire selection (CS4/5)

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