If the top level of a package contains a Data folder and a Docs folder, the Data folder will be skipped. There may be further issues relating to this, relevant forum post is:
http://forums.bethsoft.com/topic/1384740-rel-wrye-bash/page__view__findpost__p__21001218
This was an intentional design choice by the developers. I always thought it was a poor choices because a Data and Doc folder combination is a very common way that people package mods, especially those who are more familiar with the OBMM family of installers. It's also very common to see a Data folder and then various options folders at that same level. BAIN's insistence that Data can not be mixed with anything else is unintuitive to me.
I've always considered it a sign of poor mod packaging whenever a Data folder shows up like this. OBMM lists BSA contents as though you're in Data, and it generally handles mod installation under the same assumption. So I guarantee you that's why BAIN development treats this the same way and skips it.
Yet despite every installation utility known to man treating this in this manner, people still package junk wrong. Maybe I just find that ridiculously irritating but I'd lean in favor of a WontFix on this one.