when I highlight the disc 2 SD card, the format in the partition tab is greyed out. Is there something else I need to do first.
I just tried an old 512MB sd card with MPTW and it looks as though it's behaved differently to what you see. When I wiped the whole card all partitions were deleted, and right clicking on the unallocated space gave me an option to create new ones. If it were me I'd now be trying g-parted.