A Confusing Situation

With regards to your situation, I agree with everyone else. She's effectively ended it, so there isn't much you can do but try to move on, as hard as that is.

With regards to being perceived as "creepy", there are several factors that could give rise to it. For example, even though anxiety is a natural feeling, strong, irrational anxiety may be seen by the other person as creepy, particularly if you seem anxious for her attention and approval. This is doubly true if you appear to be fixated on her. Since desperation can be creepy, I think it may look creepy when this anxiety is mistaken for desperation.

Using surrashu's e-stalker acquaintance as an example - the stalker was desperate enough for the girl's attention and approval that he is constantly messaging her and telling her things that he thinks she'll like, and she thought that was creepy. Of course, this is conjecture, but to me, it makes sense. (Or maybe he was just desperate in general, lol).

I'm not saying you're any of those things, of course - I'm just saying this so that hopefully, it'll help you make sense of all of this. As surrashu said, there's a very subtle difference between being friendly and being creepy, and not all of us know when we've crossed the line, since the line can vary for different people!

Also, having good social skills will help you avoid being looked at as creepy. Knowing basic body language and physical social cues is helpful - for example, I know not to stare and make a person feel uncomfortable, but I'm constantly surprised but how many people like to STARE (I find them mostly at anime cons, lol). There's a reason why creepy people often have poor social skills.

Again, I'm not saying that you're that way, but if you're being "eaten up" by being misconstrued as creepy, why not banish that worry by reading up about how to make people feel comfortable? (That's something I should do, too - people don't think I'm creepy so much as they think I'm intimidating).

Lastly, having many friends of different genders and backgrounds will help with that. Like surrashu, I know that what I learnt about creepiness was conveyed to me by my female friends and their bad experiences with stalkers, and through a lot of social interaction, I learnt how to present myself in a better way, too.

I think it will be really therapeutic for you if you can get more friends in your classes. I realize this may be easier said than done, but it really is worth a try - that way, you can ease your loneliness and feel better about yourself. Good luck.

Jam it back in, in the dark.