What is the difference between those questions and which one is the correct form?
"Why are you still in my office?" is the correct form.
"Why do you still in my office?" is grammatically incorrect. Because of the word "do" - the person has to be doing something in order for the sentence to work. So, since the word 'still' is not a doing word, that sentence doesn't make sense.
However, it would be correct to say "Why do you stand in my office?" - because stand is a doing word.
Both could be understood as meaningful, the first in two ways. Whether any one of them is correct would depend on whether the meaning fitted the circumstances being described. The possibilities as I see them are:
Why are you in a state of motionlessness in my office?
Why, when I've asked you to leave, have you not left already?
- Why do you distill liquor in my office on a regular basis?
Here, 'still' is used as a verb - see definition 3, in the second set (not the first set) here.