I've seen this both in gedit and nautilus-cd-burner, so it seems to be
a file selector issue. To reproduce:

1. start gedit
2. type something
3. select file -> save as
4. This defaults in the home folder, where we want it, so just type a
name, like "test.txt"
5. Click on the Save button
6. Instead of saving, the dialog is still there, with the folder
changed from Home to Desktop.