If it persists, try a different body mod (Although I've not heard of this problem with CBBE at all), I'm using UNP Base / Better Females by Bella / Cover Eyes with zero problems.
Lol it was late when i wrote the OP, but now that I think of it i had noticed the problem before i had installed them with the carriage drivers in the extra towns.
But if we're on the issue of body mods i have a strange problem with female feet. They dont match up to the rest of the body and have strange shadowing on them. This issue was around before i started using CBBE. In fact i decided to use CBBE to try and fix it.
http://i1022.photobucket.com/albums/af341/charon711/ScreenShot10.jpg
http://i1022.photobucket.com/albums/af341/charon711/ScreenShot9-2.jpg