Are you working with one huge glossary or Includes?

Are you expanding with marker keys or the spacebar? The spacebar turns off some features that you would expect to work for you.

Make sure you have downloaded the latest revision.

With sort by short code selected, your entries are going to sort first by how many letters there are in the short form. It may appear entries are out of alpha order because of the number of letters in the short form. Understanding this may help with where you want your entries to appear in the advisory.

How are you setting your number of lines? Are you going to the link dialog box and setting the default there or are you right-clicking the Words or Phrases bar and setting the number there? It does make a difference where you set this up.

Numbers in short forms can easily conflict with how you choose that entry in the advisory. If you want to select an entry with the number of the line, there may be a short form in the glossary with a number and that will be the entry that expands instead of the line number.