It sounds like you might actually have homogeneous parts (multiple
parts that are identical in the same package) instead of heterogeneous
parts (multiple parts that are different in the same package). You probably have the Auto Reference (Options -> Preferences -> Misc tab) enabled. OrCAD thinks the second part is a new one, so U2 instead of U1. You can edit the part number so they match. Also, you can choose which designator (A,B,C, or D) by selecting the part, right clicking on it, then choosing Edit Properties. You may want to disable the Auto Reference and let the Annotate function do it for you, since the board layout will likely change which designator is used anyway. If you are concerned that you have multiple parts that you don't want swapped (U1 = U2, but you want the four parts in U1 to be wired together and the parts in U2 to be wired together), you can use the User Assigned Reference and relabel them later, if necessary.