If there is no underlying organicity (make sure to rule-out), and the issue is presumably behavioral:
1. It is possible your cat wants/needs to "claim" her
territorial space. For that reason, she may be bickering with her cat-brother more often (plus he is already initiating aggressive behavior toward her) and scratching on your doors. Stress-related issue/feline territorial issue. Especially since she is scratching on your bedroom doors at night (and not on other doors in your household).
Your bedroom is likely identified as familiar home turf; whereas your parents' home is not "her" home turf, and they are not "her" cat parents. So, it is not surprising to learn she doesn't scratch on the doors in your parents' home or on your roommates' doors. It sounds as if your household is pretty full - with roommates and other cats. Pheromone is located in glands on the pads of your cat's paws - to mark "her" territory - so when your cat scratches on the doors in your bedroom, she is marking "her" territory. Scratch-scratch-scratch - this is "my" space and I need to claim some territorial space just for "me."
2. Have you considered some additional one-on-one quality time and/or enrichment for your cat? It's worth noting your cat runs away when her scratching behavior causes you to get out of bed (presumably to confront her unwelcome scratching behavior). Does your cat have access to a vertical cat scratching post? Some cat owners have placed two-sided sticky tape on their doors to discourage unwelcome scratching behavior. It might be worth a try (unless the issue is strictly a "territorial" issue).
3. Like many humans, cats grow bored and become easily bored with the same old cat toys (as well as an absence of one-on-one quality time with their primary care givers). This is especially true when cats are in the mood to be "social" with their beloved cat parent and expect your undivided attention. You know ... pay attention to "me" right now. Some undivided one-on-one "me" attention before you go to bed at night and/or extra enrichment might help.
Of course, I defer to the comments/ideas from everyone else in the veterinary forum - many veterinary posters are well-qualified feline experts.