She's probably just scared. When my family got our newest kitten, she was only allowed in my room first just so she wouldn't be freaked out by everything all at once-and we already a had a cat and didn't want them to be alone together during the day because we didn't know if they were going to get along-which they got along just fine.
But when I let the kitten run around in my room when she first came home, the first thing she did was run under a chair. She got better after a little while, and within the first couple days was running around and wasn't scared anymore.