I have found that there are too many places to change the layer/color of objects. For instance, you can select an object (an alignment, labels, etc) and change the main layer to whatever you'd like. But that doesn't necessarily mean that you have moved it entirely to that layer. There are ways to change individual settings in their styles. While this provides a lot of flexibility, it's more places to have to find things.
I think there should be a coulple more options in the layer settings for civil objects:
"Current" —sets object layer to current when created
"ByStyle" —sets the object layer to the layer set in the style
I would use "ByStyle" for everything. I mean, really, I don't want all my pipes on the same layer, I don't want all my pipe labels on the same layer, I don't want all my surface labels on the same layer: setting the object to match the style would be ideal.
For your situation, have you tried setting all your style layers to 0 (zero) layer? This may help, depending on your workflow and how things work in your office. I believe they will display as per the object layer if the style is set to zero.
Mark Green
Working on Civil 3D in Canada