I'd like to know whether sdformatter does the job. I suspect it may face the same limitation as Windows itself: only seeing the card's first partition (in the case of a ROM-on-SD or CWM card, a very small boot partition).
The simplest solution for me after trial and error was to use the graphical 'slider' interface in
EASEUS Partition Master (free) to delete all partitions except the large storage partition and then drag the ends of that partition to take up the unallocated space.