Hello Mathias,
Starting from version 1.2 PhotoScan utilizes yaw, pitch, roll during alignment, georeferencing and optimization processes, since we've got many requests about that. Version 1.1 and earlier were not sensible to the orientation data.
So if you have very incorrect orientation data I suggest to use low orientation accuracy (like 180 degrees, for example), or just not load the angles to the Reference pane.