Comment 3 for bug 67314

Maybe I've found the reason for that "feature". On my system I've installed ubuntu with a near complete kubuntu set of packages (so it is a gnome+kde system), my desktop is KDE.
I found that in my root dir there's a symbolic link named ".hidden" that points to "/etc/kubuntu-default-settings/hidden-root". Deleting or renaming this file make my system behave as expected letting me browse my filesystem freely (without checking the "show hidden files" on the various browsers).
The file "/etc/kubuntu-default-settings/hidden-root" contains a list of directories "obscured". Don't ask me how this can interfere with Gnome or GTK+, really don't know....
All those settings were put in the "kubuntu-default-settings" package.