Most cameras make a note of how they were held in the image file (in the EXIF information). FA is trying to be helpful and automatically rotates photos that the camera says are rotated. My guess is that you rotated the photo yourself and the program you used didn't update the EXIF info to say that it's now with the correct side up.

There are tools to change or wipe this information in the file or maybe the program you used for rotating can also do this.

thanks :p