Version 2.6 separated tournaments and layouts. They are now saved independently of each other.
However, in order to remain backwards compatible, the software recognizes when you load a tournament from an older version of the software (which will contain the layout as well), and asks you if you want to load just the tournament or both the tournament and the layout.
When you save a tournament with version 2.6, it only saves the tournament.
Since we're on the subject, I added a preference in the final 2.6 (not yet released) that allows you to specify if you want to save layouts as part of tournaments or not. I've also added some text to the "success" dialog you see after loading a tournament that will let you know whether or not the saved tournament had a layout, and whether or not it was loaded.