To replicate:

 1. Start gnome-screenshot.

 2. Choose a save directory, but type it into the "Location"
    box. Don't choose a folder by clicking to it (that doesn't seem to
    trigger this bug).

 3. Notice that the chosen save directory is shown in the "Save in
    folder" area, then press "Save".

 4. The new file is saved into the home directory (or whatever
    directory gnome-screenshot has last considered valid), not the
    chosen directory.