You're right, it doesn't fit. Now I recall that rates of red-green colour blindness are exactly predicted by whether one or both must be defective (7% for boys, .49% for girls). Both being active but the defective version having no effect would explain the evidence, but doesn't fit the Barr body theory... it would need to know which one to choose (and it wouldn't be "random").
X-chromosome inactivation is actually consistent with X-linked "recessive" conditions, but it's a little tricky, and the wikipedia page doesn't really explain it. Basically, X-linked phenotypes aren't dominant/recessive in the same way as the others. Usually, dominance takes place between chromosome pairs within each cell. However, with X-chromosome inactivation, dominance takes place between cells. For example, women who are labeled "carriers" for colorblindness actually are colorblind in half of the cells in their eyes, but the other half are sufficient to perceive color almost as well as non-carriers.