After editing preferences, next file is saved in the wrong folder

1. Open the "user preferences" file by pressing ⌘,
2. Save the file
3. Open a new tab by pressing ⌘N
4. Save this file

Result: the save dialog defaults to
"~/Library/Application Support/Sublime Text 3/Packages/User/"

Expected: the save dialog should keep defaulting to the last folder I picked myself  (in my case, usually ~/Desktop/ or ~/Documents/)