I'm running version 4.103 and have been very happy with it. However, it's probably time to upgrade since there are now 5 versions subsequent to my current one.

I have run across threads indicating that the new versions have changed the directory structure for the ebooks and some people have had problems. Can someone please elaborate on this?

There are no changes to the directory structure between 103 and 108, Read the changelog for a complete list of changes.