What types of settings are you talking about?
Do you log into the console and then execute "startx"?
I don't know if the HOME variable is read by kde or gnome to determine your home directory. It might be an interesting experiment to:
- Create a directory in your home directory (i.e. ~/home/home2)
- Copy needed files and directories there: (i.e. cp -R ~/.bashrc ~/.profile .xinitrc ~/Desktop ~/home/home2
- log out of kde.
- run "HOME=$HOME/home2 startx"
If anything uses /etc/passwd to determine your home directory, then things may break down fast.