I have a family that I have been playing for a while. For some reason two out of three children have non-CC skin when both parents have CC skin. This is really aggravating. Anybody know why this is happening?

If your CC skins are geneticized this can account for it. The skintone the child gets is on a spectrum (skin shown can be any of the skins with a value between those of the parents), whereas hair and eyes can only show one of two values - one value inherited from each parent.

In the case of hair and eyes, the dominant colour will show up unless the colours are on the same LEVEL of dominance.
Eg: black or brown hair dominate over red and blonde. Brown or dark blue eyes dominate over light blue, green and grey.
If the colours are at the same level (eg kid inherits one green eye gene and one grey eye gene) the colour shown is picked randomly.

Skintone is all on the same level with the exception of non-geneticized skins and also alien skin. These dominate over "normal" skins.
Say you have a mum with S4 skin (the darkest) and a dad with S1 skin (the lightest). The child could have ANY skin within the range (including S1 and S4. If there are CC skins within that range they can be shown too.