Kitti has it right. The total period of absence cannot be more than 12 months including any annual leave or LSL. I actually think this is pretty fair. Some people have 13 weeks LSL and loads of annual leave so if this wasn't the case then in theory you could have someone out on leave for 15-18 months! Bit unreasonable from the employers point of view.
As mentioned you do have the option to request up to additional 12 months leave after the initial 12 month period but it might not be accepted. If you do ask to use your three weeks leave at the end of the 12 months, it is likely they would ask you to do this option and apply for the extended leave.
Sorry it's not the answer you were looking for but HR have given you the right advice.