Paint bucket and Pencil color fill problem

Hi,
I'm coloring a comic book and I'm having an annoying bug with CS4.
Say I want to color these bushes:
I put the color on another layer set to Multiply. Using the Pencil tool (no anti-aliasing), I close all the gaps.
Then fill it with the Paint bucket (anti-aliasing off, contiguous, sample all layers) using the same color.
Now say I later decide to change that color; naturally I'll use the Paint bucket.
This is what happens:
As you can see the pencil strokes are still there, as if they were a different color, even if they're not!
But on closer inspection, it turns out the CMYK values are off by 1%. I have no idea why this happens. The tools are all set at the exact same color and opacity.
Someone posted a thread 9 months ago about this problem but it wasn't solved: http://forums.adobe.com/thread/781035
He says it also occurs on CS5.
I can only assume it's a bug. Help?

I just tried with the pencil set to Multiply, and it happened. And contradicting what I said earlier, the problem happened with Normal as well.
Well, here's another update: the real culprit seems to be the paint bucket tool. I experimented with color samplers to precisely measure the CMYK values. This is completely bizarre:
The paint bucket will occasionnally fill with a color that is off by 1% from the intended color. It seems to happen randomly, but more often with darker colors.
Check this out:
Sampler 1 is where I closed the gap with the pencil. Sampler 2 is the paint bucket fill.

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