I went from windows machine to PC-BSD 10.3 about 2 years ago and then to TrueOS. At first I really liked it, specifically ZFS integration. I consider ZFS a hidden gem of data storage. After the second update troubles began. Every time there was a new system update, some software was quietly removed from the system. If I reinstalled it by hand again, usually something broke. I guess it wasn't compatible with the newer…
As to software disappearing. I think what might have been happening is that you'd go install something, but the upgrader had already run and created a new boot environment for the update based on a snapshot from before you'd installed the new pkg. So just as soon as you rebooted into the new BE, you'd "loose" the package. This is one of the reasons that they changed how the updates work, and only create the new BE when you're rebooting. I personally hate this, as I'd rather re-install something than wait 1/2 for the update to re-install pkgs in a singleuser-ish environment.
I second the notion that you might want to consider switching to Ubuntu, rather than going back to Windows. I've run ZFS on Linux for years on my old desktop (now my wife's) and never had a problem. The only "issue" I had was the transition from 14.04 to 16.04 was a bit rocky, as 16.04 includes ZFS natively, rather than using the zfs-on-linux ppa.