Like others have said, you should use something to (temporarily) make the windows more visible. Rubbing a bar of soap on the outside works, or drawing lines on the inside with washable marker. Painters' tape could also be used to make lines. Also take her up to the windows and tap on them with your finger - encourage her to tap them with her beak, too.
Also, of course, be careful of startling her. She's in a new place, and she's still a baby (and going to be clumsier than an adult). Caiques are also heavy bodied birds and just naturally the most graceful fliers, so it can also help to show him safe places to make 'emergency landings' near any especially problematic windows. It could be as simple as occasionally placing her on a chair or other piece of furniture near the window so she learns it is safe to land on if she finds herself headed toward the window.
Her flying should improve as she gets older and more familiar with her surroundings.