I can't say for sure because I haven't actually seen you two interacting but it's not that uncommon to hate (or strongly dislike) someone and at the same time like them. Two people I've had crushes on in the past were both horrid people in some ways (arrogant, condescending, patronising etc.) and yet undeniably attractive in others (physically, funny, intelligent), it just depends on if you feel their good qualities (the attraction, conversation etc.) are worth your distaste for them. Nobody is perfect after all, maybe you're always catching her at her moodiest? Have you seen her interacting with other people, or outside work?
Maybe you should spend some time apart from her to have a break and re-evaluate your relationship with her. Perhaps you're attracted to the challenge? Or the way she's willing to argue with you, stand up for herself (even if she's wrong). Remember, some qualities can easily be seen as unattractive to one person and attractive to another so just give it time.