I have finally solved my problem and would like to thank everyone for their help. As I said in my opening statement this external was used on an old PC and for some reason this lead to permissions issues. After going through all the subfolders to change the permissions for the files the drive's used space is now correct on WinDirStat and when selecting all the files and clicking properties.
@Psycogeek - you were correct in saying that MyDefrag shows the files, thanks for that, unfortunately due to the files being in a folder that I had used frequently and had permissions to I wasn't able to determine that they would be missing. Plus 675GB of files is hard to go through :P
@Alexey Ivanov - The files were viewable in windows explorer like you said but WinDirStat and windows explorer apparently do not include files with permissions from an unknown source - thanks for the help.
If anyone else has this problems it could be down to this issue. File explorers and visualisers seem to have trouble examining files that have different permissions - You have to remove the unknown user's permissions and change the permissions to your current system - in my case this was arthur-PC/arthur rather than a long string of characters. As there are already guides for this I will post a link.
http://answers.microsoft.com/en-us/windows/forum/windows_vista-files/how-do-i-change-folder-and-file-permissions/465f2b42-63dd-4486-8dd1-c870290efeed
First answer is correct. - remember to click subgroups and folders, because I did not do this when orginally changing permissions I could view the contents of the folder in windows explorer but not subfolders and you have to click each and every one to gain access to it.
Thank-you to everyone for your help, I hope this answer can help people that might have the same issue.
Arthur