Really hard to say with the limited information provided.
And to be clear, you don't write a fade using automation. You *create* automation events so the fader moves automatically, right?
That said, I haven't had any issue with periodic failure of automation. You can enable/disable it. Perhaps you are accidentally hitting that shortcut?
If you go into Keyboard Shortcuts and search for automation, you'll see that hitting the J key toggles Read.
That's my best guess.