It has been confirmed, somewhere around here (the forums, overall), that this is a visual bug with the UI.
The buffs are still there (IF they *should* still be in effect). You can reference your stats to confirm.

And it's not just affecting the Arcanist.

I was fishing with my Necromancer yesterday, and using the Artaeum Pickled Fish Bowl (the fishing buff food), which has a two-hour timer, and every time I logged-out, the buff would be gone from the main screen when I logged back in, and missing from the character screen, as well.

But comparing my unbuffed stats to my buffed stats showed that the buff was still in-effect for the proper duration.