The problem is based on these circumstances:
1. You have X2Go installed from packages.x2go.org. The version string
starts with: 4.0.1.18-0
2. The version of x2goserver in the fedora 20 updates repo has a
higher version string: 4.0.1.18-5
3. You have the package x2goserver-extensions installed from
packages.x2go.org. This is normal.
4. The x2goserver packages in Fedora 20 (both the base repo and the
updates repo) do not include the x2goserver-extensions package.

Orion,
It looks like the files that are in the packages.x2go.org
x2goserver-extensions package[1] are included in the Fedora
x2goserver[2] package, correct?
if so, I think Ura can solve this problem by removing
x2goserver-extensions, and then running yum update.

or:

yum shell
> remove x2goserver-extensions
> upgrade
> run

I could probably have the Fedora x2goserver package provide x2goserver-extensions to help with such situations.

-Mike#2

[1] http://packages.x2go.org/fedora/20/main/x86_64/rpms/x2goserver/
[2] http://koji.fedoraproject.org/koji/buildinfo?buildID=602993