If you create a new book from the template chooser, do the page thumbnails show content, with just the sample content?
The text wrap is expected behavior with epub templates. The wrap options will always be disabled. Control the placement of the image using styling applied to the paragraph styles.
If viewing layouts, the layout should show Apply Changes button if the layout is edited AND the layout is in use in the book.
Isolate the the app vs the book file by creating a new test user (not the guest), signing in to the new user and see if on a new book the thumbnails are empty.
If yes, reinstall iBooks Author. If it works properly on new book on test user and not on new book on original user, I’d quit iBooks Author after saving and delete the plist preferences for iBooks Author and reopen after deleted and check again.
Plist files are in ~/Library/Preferences folder.
Sort by list view in Finder and locate com.apple.ibooksauthor.plist and anything else with com.apple.ibooksauthor. Delete the plist files.
iBooks Author should not be open when doing this. Restart iBooks Author and check again.