This is a common issue with wearing any of the layers that the baking service combines layers into a single baked texture. The underlying issue is that they are not baking in the layer order you wish them to bake in. I have not found a wardrobe solution as yet that is 100% full proof and not sure anyone else has cause its not an issue with wardrobe or RLV functionality.
The reason this occurs is because in most cases the skin layer is using a tattoo layer, the end result is your tattoo (facial tattoo/cosmetics) and/or hair base which also uses a tattoo layer is actually been baked under the skin layer. You can right click yourself and edit your outfit were you can then move the layers up and down in the order of baking but this does not mean that order will be the same next time.
In an ideal SL world, it would be great if cosmetics, hairbases and facial tattoos etc were created by content creators using the new Universal Layers instead of Tattoo Layers as this would resolve this issue.
Alternative is to source a skin that includes both body and head in the skin layer. There are a few skinners who do this however most do body skin using the skin layer and head skin using a tattoo layer.
Ultimately, the real cause of this issue is that LL didn't really take into account how skinners made body and head skins for mesh bodies and heads when they introduced BoM and really didn't make it clear as to how things stacked and worked. They should have introduced a head skin layer that sits on top of the current skin layer but under the tattoo layer.
I go more into BoM Layers and Wardrobe in My Blog Post
The following graphic should provide a visual of what is happening.
