For my own sake of remembering, I thought I would post this here. After much travail, I finally have it figured out!! There are two types of fills in inkscape. One that is Even Odd fill and the other that is non zero.
I won't bore everyone with the differences between the two, but make sure you have the left fill option of the fill and stroke dialog box checked if this ever happens to you.
Exclusion works as well, but I would like to bypass the Boolean operations if possible (see green arrow).
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