I believe your problem is not directly caused by upgrading from 3.0 to 3.1. It is more likely that there is a change to the theme that you were using on 3.0. It may not have been migrated over properly. You might need Administrator access to fix it. Something similar happened to me.
We have installed the Essential theme, and defined some book customisations on the Essential Theme General page (Site administration > Appearance > Themes > Essential > General) in the Custom CSS section at the bottom. These customisations may not have been copied over when you moved from 3.0 to 3.1. Alternatively, new customisations may be breaking your book appearance.
If you don't have Administrator access, you can still fix your problem by adding some CSS directly into your book pages, although it is a pain, and I don't recommend it. Something like the following might work (copied from http://stackoverflow.com/questions/11737266/what-is-default-list-styling-css):
<style type="text/css">
div.book_content ul {
list-style-type: disc;
list-style-position: inside;
}
div.book_content ol {
list-style-type: decimal;
list-style-position: inside;
}
div.book_content ul ul, div.book_content ol ul {
list-style-type: circle;
list-style-position: inside;
margin-left: 15px;
}
div.book_content ol ol, div.book_content ul ol {
list-style-type: lower-latin;
list-style-position: inside;
margin-left: 15px;
}
</style>