This issue goes back awhile ago. We are using WF3 and the problem with assembly cuts is quite the same.
Components are split in several rows in BOM, because mass properties are calculated at assembly level. Even though the parts are on the part level the same, mass gets calculated considering assembly cut and then updated in the part i.e. repeat region.
Workaround to this is to regenerate assembly to calculate correct masses for each part, then open part relation dialog box and comment the line where mass is calculated, switch to the assembly again, calculate masses and regenerate. This way assembly mass calculation does not influence the mass of each component and repeat region shows appropriate pieces of parts which are subject to assembly cut.
You only need to bear in mind, that mass calculation in the part is commented out and you need to repeat above procedure when you redefine features which affect mass of the component.