i found out what happened to the flax etc by planting more in different places.
turns out that the flax goes green if not getting enough sun, then dies , well disappears.
I made this post thinking it may be something like this, but started blaming myself with proxy server issues with steam client.
ie if i had been using a browser, usually watching eso's builds on you tube, the browser turns on the proxy server which prevents steam from loading up.
if during the game, i chose to watch esos build eg the one on top of a tall rock in the plains biome, then the proxy gets turned on again, which i suspect causes the syncing failure with steam if i close the game then steam to go to sleep or what ever.
the flax and barley were planted under the floor way way above the ground on this rock so sun does get to the plants but the game must only consider 90 degrees straight up like it does with rain so even if you see sun on the plant if it is directly under your building no matter the height it counts as blocking the sky.