After some helpful advice from the people on irc I have resolved my problem. The mod_security module on my hosting server was the problem. The module acts as a script firewall and blocks certain word strings. Its aim is to stop comment spam by blocking URLs that people put into the posts. It does this by processing the entered text before the main wordpress scripts store it on the site. If an blocked URL is detected the script returns a 412 Precondition fail.
This was the error I recieved when I was trying to update my black list. It was detecting the blocked URLs and stopping the list being updated. Removing the blocked URLs the list was able to process as normal and blacklist sites not covered by the mod_security module.
I hope thats somewhat clear.
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