XRTSUB assumes that neither the source box nor the background box overlap any of the struts or the central circle. If this isn't true, e.g. if your background file is a spectrum which has been taken in an annulus around the whole image at a large radius, then the program will overestimate the area of the background box. This problem may be alleviated by using a spectral image as the background file (see the advice section on extended objects).