Odd disk space behaviour

There can be many reasons for this. The file structure use 16K blocks, so each file or part of a file will occupy a minimum of 16K no matter how small the file. If the file is 16,385 Bytes, then it will take two blocks (since it is 1 Byte over the 16,384) or 32,770 Bytes and be reported as 33 K even though windows reports it as 16K. If you are using Windows Vista or Windows 7 the thumbnails used to display the files also will take up space, but not show up in the directory.

Two 500GB drives in X-Raid will give you a redundant volume of around 462GB (Converting 500GB with the 1000/1024 byte conversion gives approx 488 less the 26 GB for overhead gives 462). As to why the volume shows up as 407GB used, if you list all the files and sizes, the file size on disk will be in blocks of 16,384 Bytes not the 512 Bytes found on a PC disk. Then there are the hidden files on the disk. Windows Vista and Windows 7 stores thumbnails in the same folder as the file with which it is associated. These are hidden files and do not show up in listings. While they are generally small files, each one will take up another 16,384 bytes minimum.

When I had a 500GB volume on my NV+ (2 x 500GB drives as you have), I used to try to figure it out and finally gave up. The ability to use larger drives and larger volumes and the newer operating system are just going to take disk space. I would just update to the 2x2TB drives you have and enjoy the additional space.

Don't forget to update your backup before you start swapping drives (of course you have a backup) just in case something goes wrong. Murphy is always lurking.