CF memory shrinking

I have several Extreme III cards, 16GB and 4GB.  I notice lately that my cards are full in my Nikon D3 but really they are only holding a fraction what they used to hold.  Example my 16GB card only fills to about 4GB.  I always reformat in the camera before use, is there a way to recondition and reclaim the memory space?

Try formatting your card using ‘HP USB Disk Storage Format Tool’.

http://software-files-a.cnet.com/s/software/11/12/08/56/SP27608.exe?token=1340183011_6657b6f9a607b66454981984a569a84b&lop=link&ptype=3001&ontid=2094&siteId=4&edId=3&spi=e2f7c27bbd7c29e308251b4858306f90&pid=11120856&psid=10974082&&fileName=SP27608.exe

it will recover the missing space in ur memory cards.