I have a system built loosely on LFS linux. I am currently running XFCE 4.12 desktop.

Everything works as expected, unless I suspend the computer. After I resume from suspend mode, I am no longer able to shutdown my computer. There is only logout option available.

I can see the issue in my .xsession-error file, where it reads:

When I log out and log back, everything works again as expected.

Can someone point me to where the resume issue might be? I probably have something mis-configured regarding dbus and consolekit.

Make sure your user is in the "power" group if not create one.
Then suspend is different than sleep so make sure a boot time you told the
kernel where your going to resume from.
mine is
sda4 is my swap partition.
As for for suspend to ram. Sleep.

Then again it isn't reloading console kit.
This means it is unable to create a socket.
Because there is one already in use. But it is stale.
When you logout it clears that /tmp/socket
log back it it creates a new one.
I hope this points you.
Good place to also look at and understand D-Bus
~/.dbus