Perhaps some of those were different formats of the same 'book' (ePub, PDF, mobi, etc.)? I'm back at my Mac, I'll take a look, I still have a copy of an earlier version...
Later...
I found that there is a still newer version available.
However, the three versions I have seem identical in the way the display my 'books' in the main page list. I see 33 items in each. Even the columns are the same which, to me, implies that all the versions are using the same plist file.
Perhaps a partial screen shot of your different versions could help. There are some prefs for setting font sizes and line spacing, but I don't see how that would affect the
total number of rows.
Here are screen caps of the two versions. As you can see there is a big difference