This question already has an answer here:
Realize, later, that you should have added an edit summary and did not (or that you just want to change it).
Add or change edit summary.
Press 'Save Edits'.
Edit summary is not saved.
Make it so that edit summary changes are saved (already asked for here: Editing edit summaries)
Make it clearer when it will not be saved (and give the warning before a user goes to the trouble of typing out a new edit summary).
The way it works now a person could make new edits in order to save a new edit summary, but that should not be required as it just encourages fake edits.
For 2., all that would be needed is an pop-up alert when the user clicks on in the edit summary field without having made any new changes. Something along the lines of "This edit summary will not be saved unless new edits to the post are made."
Here are some more details, in case this is not the way it works all of the time:
I made an edit (actually a roll-back on my own post), but did not know there was a comment field for that. About an hour later, I found out there was such a thing as an edit summary, so I hit "edit", added one for the roll-back, and pressed "save". I happened to think I should make sure the edit summary stuck (since I really wanted to make sure the original editor got to read why I did the roll-back) and when I hit "edit" again it turned out that no, it didn't. The edit summary was gone.