I've finished the game and get all achievements except the 'Contamination'. I don't know what is missing. Is there anyone can help me?

Do you know?

I completed the game a day or so ago. I noticed today that the last three achievements didn't register, so I went back through to grab them. (I'm guessing that could be related to me tabbing out to see what I was missing on the Thumper date puzzle.) Bug 1) At any rate, I was riding the minecart and rode straight through the closed door that's opened by a switch on the far side, activated by the "sarcophagus button" puzzle. (That puzzle frustrated me to no end because I didn't know if the problem was that ...

I am not given the Harvest achievement when I solve the puzzle with the thumpers. Does anyone know how to get the Harvest achievement?

I got the mine cart to the contamination point then logged off. Logged back on to find the mine cart completely gone. I thought maybe it just moved on without me. I continued complete the puzzles up to the switches with all the numbers. Got the door open and still no cart. I thought I could just walk on the rail so I back tracked looking for the carts...nothing. No cart no moving forward. Obviously don't log off you lose the cart....