Thanks, this seems to work. At least I can now change settings in programs and dconf doesn't throw this error.
Here is the output of intree:
Name : boot
Initialized : yes
Enabled : no
Starts after : None
Current : no
Allowed : root
Symlinks : svc->source db->source
Contents : /
|-(208,Enabled,classic) tty-earlier@ tty12
|-(up,Enabled,oneshot) system-hostname
|-(up,Enabled,oneshot) mount-run
|-(up,Enabled,oneshot) populate-run
|-(up,Enabled,oneshot) mount-tmp
|-(up,Enabled,oneshot) populate-tmp
|-(up,Enabled,oneshot) mount-proc
|-(up,Enabled,oneshot) mount-sys
|-(up,Enabled,oneshot) populate-sys
|-(up,Enabled,oneshot) mount-dev
|-(up,Enabled,oneshot) mount-pts
|-(up,Enabled,oneshot) mount-shm
|-(up,Enabled,oneshot) populate-dev
|-(up,Enabled,oneshot) mount-cgroups
|-(up,Enabled,bundle) 00
|-(up,Enabled,bundle) all-Mount
|-(up,Enabled,oneshot) system-hwclock
|-(up,Enabled,oneshot) modules-kernel
|-(up,Enabled,oneshot) system-random
|-(up,Enabled,oneshot) modules-system
|-(up,Enabled,oneshot) system-sysctl
|-(274,Enabled,longrun) udevd-log
|-(431,Enabled,longrun) udevd
|-(up,Enabled,oneshot) udevadm
|-(up,Enabled,oneshot) system-fontnkey
|-(up,Enabled,oneshot) system-fsck
|-(up,Enabled,oneshot) mount-fstab
|-(up,Enabled,bundle) all-System
|-(up,Enabled,oneshot) mount-rw
|-(up,Enabled,oneshot) mount-swap
|-(up,Enabled,oneshot) mount-netfs
|-(up,Enabled,oneshot) local-loop
|-(up,Enabled,oneshot) local-sethostname
|-(up,Enabled,oneshot) local-time
|-(up,Enabled,oneshot) local-authfiles
|-(up,Enabled,oneshot) local-tmpfiles
|-(up,Enabled,oneshot) local-dmesg
|-(up,Enabled,bundle) all-Local
|-(up,Enabled,oneshot) all-Runtime
|-(up,Enabled,bundle) All
|-(769,Enabled,longrun) tty-rc@ tty2
|-(768,Enabled,longrun) tty-rc@ tty7
|-(767,Enabled,longrun) tty-rc@ tty5
|-(766,Enabled,longrun) tty-rc@ tty6
|-(759,Enabled,longrun) tty-rc@ tty8
|-(761,Enabled,longrun) tty-rc@ tty3
|-(770,Enabled,longrun) tty-rc@ tty4
|-(772,Enabled,longrun) tty-rc@ tty1
`-(up,Enabled,module) boot@ system
Name : root
Initialized : yes
Enabled : yes
Starts after : None
Current : yes
Allowed : root
Symlinks : svc->source db->source
Contents : /
|-(711,Enabled,longrun) dbus-log
`-(715,Enabled,longrun) dbus
Name : boot-user
Initialized : no
Enabled : yes
Starts after : root
Current : no
Allowed : root
Symlinks : svc->source db->source
Contents : /
`-None
Name : net
Initialized : yes
Enabled : yes
Starts after : root boot-user
Current : no
Allowed : root
Symlinks : svc->source db->source
Contents : /
|-(728,Enabled,classic) dhcpcd-log
|-(732,Enabled,classic) dhcpcd
|-(736,Enabled,classic) wpa_supplicant-log
|-(733,Enabled,classic) ntpd-log
|-(734,Enabled,classic) ntpd
`-(735,Enabled,classic) wpa_supplicant