I had a simlilar problem when i was younger but not too sure if this could be the same thing. I use to wake up getting scared and ill be sat up with my eyes open but still actually asleep. My mum took me to the doctors and was given some sort of medication. Sorry i cant help you more your probably best taking her to the doctors to make sure but it could just be that she is in a deep sleep when woken so takes a few minutes for her to realise shes actually awake. Obviously thats if she is woken.
She may not actually be awake yet. Don't panic. If I wake my daughter from a nap, she sometimes acts scared or upset for 10-15 minutes. After that little bit, she's perfectly happy. I figure I interfered with REM sleep, which would disorient anyone.