Mynex is right - I must have had too much cold medicine in me! It is indeed the distribution factor that is key - if you bought the book you can make any copy of it you desire, including typing it into your preferred file format (i.e. Lst File format). However, you do not have permission to distribute your copy at all. That means that you can't share any of the copies you have with anyone unless the owner of the copyright (Wizards of the Coast in the case of books like Defenders of the Faith) have given you permission to do so. You can share the files with other people who also own the books. There's no way to verify that people who visit a site on the web own a specific book, so placing Lst Files on the web for others to access on the web is a no-no unless you have permission from the copyright owner. That's why we work so hard to acquire permission for all the books out there so we can include them in our releases of PCGen. The nice thing about the Open Gaming License is that for material that is declared entirely Open Game Content, no permission is required (however, we will still do so since that is the professionally courteous thing to do). The only restriction we have is for material that is declared product identity - that requires specific permission. The splatbooks and dragon magazines are not OGL, therefore we need special permission from Wotc before we can include any of it.
Hopefully the above clears up your questions without getting into a technical discussion of the OGL license. If you really want to get into a technical discussion you'll need to read up on the D20 license and LGPL license as well. It's enough to make your head spin, even without cold medication!
-Bryan