This is common to horses that are new to box stalls, particularly in the rain, it makes quite the noise hitting the metal roof and it takes some getting used to – so I attributed her behavior to this, grabbed a halter and led her into the box stall and she was fine.
I feed very early in the morning – its still dark and I noticed that she was having problems finding her hay – so I called out my vet and we discovered that she had cataracts in both eyes. She was pretty well blind in the dark, and had limited sight during the day.