Ryder, What file system are you using on your drive (fat32 or NTFS) and how large is the drive? If it is a larger partition and the programs have a lot of small files (or a lot of files) then it can consume a lot more diskspace then the combined files. Fat is worse then NTFS in this respect
Also the BIOS doesn't care about HD space used/free, all it cares about is total size and C/H/S (physical specs) the OS and file system are the only things that report HD usage info.