Are you somehow trying to mix ports and pkgs? It is not a good idea, and usually do not end well. Also pkg come configured to use quarterly packages, and not latest, and ports are in general still newer than the latest packages.
If you value more stability than updates, stick with quarterly.
Xorg was upgraded recently but the problems, at least almost of them, are already solved now. Also, unless you have a problem or a specific need you do not need it, and it is not advisable to use a
xorg.conf in general.
If you are building from ports, better use
ports-mgmt/synth or
ports-mgmt/poudriere to do it. As reference
Synth and
Poudriere.
With the amount of weird random problems you are experiencing, I do believe you have hardware problems, it seem so memory issues - or at least low memory.
Do check disks and memory.
FreeBSD uses memory differently than other systems, what means your memory may have problems since years and never appear on Linux/Windows but give you a lot of headache on FreeBSD.
Again, take a look on what I said before about RAID and ZFS, if you are using RAID and ZFS.
If you are using a custom make.conf, remove it and try to make the things work with the default settings, and without using
-j
with
make
.
And do not forget to carefully read the FreeBSD
Handbook.