My dog, a 5 yr old amstaff is clever I'm sure, she always knows when you're not looking and when you've definitely left the house etc! But often, although she looks like she wants to obey a command, she follows a different command to the one you've said. Like I tell her lie down, and she went to come to me, but then stopped like she knew she'd gotten it wrong, with her head down and everything so I don't think this is plain old defiance. It's not her hearing either, this only happens sometimes, but then again she goes through phases of it happening maddeningly often. Any ideas?

Some dogs are clever and just like to mess with you but your girl may just be confused by the hand motion or verbal command you are using. Its very importatnt to always, religiously use the same one word command. If she still does this and you are certain you have consistently used the same command she may just benefit from more training. I train my dogs every day and every day is different. With a dog you must establish yourself as someone she respects every day. Dogs do not recognize anyone as "leader for life." How much time do you spend for training and for exercise each day?

Adding a command before the dog understands a behavior is not black and white.SO We want the dog to look at a command as part of the linked chain that leads to a reward.

If a dog is confused over commands it's because the person giving them is confusing the commands.
If you say 'down' sometimes and 'lie down' other times, lie down might be construed as 'come here' just because it's two syllables. And as said, gestures are important too.
A dog shouldn't be hanging her head when responding to a command. Heap praise on her when she does the right thing, and don't punish her for doing wrong.

Remember that dogs don't know English, so they will respond better with a hand command. If you are using the same hand motion (unintentionally) then it can get quite confusing.

Try using a different hand command with each verbal command that you use. Some that I use are: When I want my dog to sit, I put my index and middle fingers up like a closed peace sign, when I want them to lay down I either point to the floor, or make a sliding motion with my hand (hard to explain, I know). When I am using the command stay I put up my hand palm facing them like a crossing guard saying stop.

Joy makes a good point, try to use one word commands, remember “sit” and “down” are two different commands. So when you say “Rex, sit down”! You are giving two different commands. I have several amstaffs in my house now, loving, wonderful smart breed. They are always willing to please. The easiest way for them to understand what you want from them, is for them to learn the action and then the command. I hope that makes sense.