I've seen that before, when Repair Permissions is run from a different start-up disk (permissions are matched to the current system running).

Just restart in Safe Boot Mode (hold down the shift key right after the start-up tone), login to your usual user and run Disk Utility-Repair Perms again.

This will reset the perms back to your usual set.

Thanks.

So it's unlikely to be anything to do with LW then?

When I think about it, I think I may have clicked on the 2nd HD icon rather than the first.