My female Apisto Baenschi did pretty much the same thing at first, mostly because her mate is a big meanie who claimed the entire tank for himself. I was really worried about her for the first week or so, I thought she was going to be traumatized (or worse). Little by little, she settled in and I started seeing more of her. Now (3 or 4 weeks later) they have seemed to form a couple, and she has truly changed...no more hiding in corners and caves, and even has quite the little 'tude going on. Her mate still chases her (and is still a tyrant), but she is no longer cowering, sometimes she is even the instigator. And now, more often than not, they hang out peacefully together. I actually can't believe the difference. I was convinced I was going to have a dead fish on my hands.
How long have you had her? Maybe she just needs time to settle in, like mine did. Having her own little coconut cave helped immensely, made her feel secure. But now she no longer hides in it, she hangs out there with her little head poking out (keeping an eye on her man, I am assuming).