Dammit, time to get technical
I'm a planning consultant by profession so let me just clear these figures up for people.
Flood Risk is split into several categories, most of which are irrelevent, but the important ones here are;
1 in 100
1 in 200
1 in 1000
These are basically flood levels set by the Environment Agency and based on a huge computer model of flood events, taking into account rising sea levels from climate change and all that jazz. When you apply for planning permission in a flood area you need to demonstrate that you can sufficiently mitigate against these levels. (you only have to mitigate against the ones that are considered relevent, so if you live in the middle of Birmingham you wont have to show the same mitigation as if you live on the beach. 1 in 1000 is only ever normally applied in the nations largest flood plains, Bristol etc.)
Think of them as risk rather than timescale. i.e 'there is a 1/100 chance of these levels being reached in any given year', rather than 'this will happen on the dot once every 100 years'
1 in 1000 is basically a freak event. It's used normally to test flood defences (i.e those defences are fine for 1 in 100 and 1 in 200, but what happens when we have a freak 1 in 1000 event and the water comes over the top of the defences).
Simply put, the 1 in 1000 referred to is an Environement Agency prediction model based on risk rather than a record of how many times these levels have been seen.
Right, I'll bugger off and stop being boring now.