This has happened to me twice, the first time erasing Firefox settings, and the second time erasing gnome-terminal settings. Both cases were caused by a kernel panic locking up the system. Also, both times the program whose settings were affected was in use during the kernel panic.
An important note is that these data losses have been taken place on an ext3 partition that is mounted as ext4 in fstab, so it is not a true ext4 partition.
This is taking place on fully up-to-date Jaunty.