The next time a new version will be out, it will reappear though.
There are only about 10 Silverlight updates as of right now, so once you have no other updates you can just keep checking for new updates, hide the Silverlight one, then again and again until you hid them all.
It was another Stack Overflow question which I have lost the reference to so I do apologise for not referencing it properly, but the problem is caused by the Text Box and other control styles having a fixed position of to the side of the control when displaying the validation message.
I simply had to create a copy of the style and have the popup appear at the top of the controls instead of beside it.
So, problem is there are 7 different versions of Silverlight. You can manually Hide, "Check for Updates", Options, Hide them in a loop 7 or more times.