Just wondering if he was trained in sit and down (not lie down, that's confusing :P) before you had him?
If so, and as you say he was a rescue, he may associate any kind of training with telling off. Alternatively, if he wasn't trained, and you are training him by the modelling method (ie shoving his head up and his bum down for sit)he is simply large enough to not do it :)
Just a few thoughts, I think he'd love a clicker class, it's a particularly good way of training as dogs end up thinking they are training you, so end up very willing

He may now just need boundaries, I believe all dogs are happier with these, whether they are nervous or strong minded, as it gives both types security. You could do this by simply asking for a sit before lead being put on, dinner, etc - it would be a great start.
Good luck
Lindsaiy
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