It’s a current known bug where the armor ends in inventory after loading a saved game:
http://www.unlok.ca/wiki/wayward/bug-list/
When I had the error with stats not updating on equipping gear, I found equipping then resting the character updated it fine.
However I had a game where I had used the BullBoat, ended teleporting to a random new island, and after that got error messages with nearly every action I took. The game was still playable as the error messages were only “distracting” and I could play fine ignoring them, but they were very annoying and the only way I could find to make the messages stop, was to delete the save and start a fresh game. Hopefully you do not have that same issue (fixed I think in the upcoming Beta 1,1 version, though reequipping gear after loading a saved game is something he is still working on).
In your case, had you used the Bull Boat at all? That’s the only time I really had a bad bug with the game, ever since restarting, everything has worked great (except needing to reequip everything after loading a save)