Thanks much! Sounds like I'll keep it unless I start to have issues, which hopefully I won't!

Just a quick update, I uninstalled KB2999226 and everything seems to be back to normal, performance is great again.

Glad to read that. ;-)

Another update, and probably the last one:
Yesterday both Windows and Ubuntu 16.04 had slow performance issues. It seem that the 1TB HDD was causing this problem. The HDD does not respond anymore, most of the time it does not even show in the BIOS, I can't copy or view anything. So I took it out, and now everything is normal, except for the fact that I lost all my things, on the bright side, most of them were backup copies of Steam and GOG games which I can download again, but there were a few courses and a few pictures.
Again, thank you all for the help.