Maybe he's shy and embarrassed to tell you how he feels. If this is possible, you should tell him how you feel about him.
Why is he such a weirdo? This guy flinches every time he sees me and he walked up to my table in class, said something under his breath and I said "hi" he said "oh hey" and walked off.
It could be that you resemble someone who he has had a traumatic experience from. As for the saying things under his breath, is he actually standing at your table when he does? If he isn't, and is just walking up to the table, it's likely what Alex mentioned; he might just be shy and is just trying to think of what to say. Though, if he isn't actually stopping at the table, it could be that it's the only route to take to get around to where he's going. It may be that your table happens to be the safest-looking to pass by.
There are a lot of answers to be given here, but these are probably at the top of the list. Just try thinking of why you may do those things if you were him.