Yes. My updateVM was set to custom-sys-net. I changed it to 
custom-sys-firewall, as you recommended. 

I am very unfamiliar with the command-line (thats called bash, right?) tools. 
But qubes-prefs updatevm custom-sys-net = yes. 

What I actually did:
sys-net$
yum clean all 
yum repolist all
# There are no enabled repos.
dom0/sys-net$ systemctl status updates-proxy-setup
# No such service.
dom0$ systemctl status qubes-updates-proxy
# No such service.
sys-net$ systemctl status qubes-updates-proxy
# good
sys-net$ systemctl restart qubes-updates-proxy
sys-net$ spt-get update
# No new packages.
debian-9$ sudo apt-get update
# No new packages.
Fedora-26$ sudo yum update
# 84 new packages. 

What I think did the trick:
Im not sure exactly what did it, but it must have something to do with 
1. dom0$ qubes-prefs updatevm sys-firewall
2. $yum clean all;  
3. as well as re-enabling the qubes-updates-proxy in the Qube Manager 
sys-net:settings>Services tab (which I had added and removed multiple times)
4. sys-net$systemctl restart qubes-updates-proxy


Thanks for your help, youre a Light Sabor!

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