Since my 500D was repainted water has been getting in at the base of the windscreen, presumably through a gap in the rubber. Any advice on what I can do to stop this?
Thanks

If the rubbers are in good shape, I'd suggest you to take the windshield off and put it back. Eventually with some sealent to make sure it doesn't happen again. (I'm a newbie here, though, wait for more answers..)

You can get a tube of non-setting, black sealant which is specifically for this job. You can leave the screen in and point the nozzle under the outer lip of the zeal. Then squidge down the rubber to push out the excess. I let it dry for a few days then found the surplus easily peeled away. Any remaining streaks came off with white spirit.
I think that this is a design flaw with the windscreen which they tried to put right with a drain hole on later versions.
It took several attempts before my windscreen was sealed.