My cat is acting strange - hiding under bed, not using litter box? What do I do?

My uncle found a stray cat, Luna, and decided to keep her in his garage so he could feed her and take care of her (he took her to the vet, she is up to date on every shot, flea medicine, etc.). I took her in because I know that I would be able to spend more time with her. I have 1 bedroom apartment, and I also have another cat, Pancake. Pancake is a female who is about 1 year old. She is very playful. Luna, my new cat, is a female around 6 years old (vet estimated age). She is VERY skiddish. Whenever I try to pet her, she gets nervous and runs away. However, once in a while she will jump up next to me and let me pet her (she even purrs sometimes). Both cat's are fixed.

Since Luna has been at her new home (about a month), she has been hiding under the bed almost 24/7 and not using the litter box that is right next to the bed (she goes under the bed). Pancake sits at the end of the bed and tries to go under with her, and Luna hisses/growls. Can anyone explain to me why she does that, and what I can do to help her stop doing this?

Her food and water are in the same room as her, on the opposite wall. She comes out to eat/drink about twice a day and goes right back under the bed. Sometimes I try to lure her out with treats, but she just eats them and runs back under the bed. There are 3 litter boxes in my apartment, one is RIGHT next to the bed where Luna hides. At one point, she even pooped on the floor on the opposite side of the room. Yet, when I put the litter box in that spot, she doesn't use it. Instead, she goes under the bed. I thought maybe it was because my other cat, Pancake tends to use the litter box that I set up for Luna, but how am I supposed to stop her from doing that? Since I live in a smaller apartment, I want my cats to be able to roam around with me as much as they can (I don't want to shut my cat out of the bedroom).

I need someone to help me understand why this is happening and what I should do to solve the problem!!! I have tried picking her up and having her explore the rest of the house and she runs right back under the bed!

*FYI-I know having 2 cats in a 1 bedroom apartment seems unethical. HOWEVER, I live in the same house as my landlord (she has a 3 story house with 4 bedrooms of her own), and I have a cat door connecting my apartment to the rest of the house, so they have more room to run around than in my tiny space. She is an animal lover and also has 1 cat of her own who usually stays in the landlord's area.