No they weren't scared after the flash at all. Infact the first 2 photo's are from the same squirrel, and he just stayed there for a few seconds. Markulous i like the way you've done it. Looks a lot better.
But it is fairly easy to get good shots of them. Although you need a good day with sunlight and a good spot, which my two little toddlers had found for me as they were hunting after them

But they come nearby and even eat out of your hand if your lucky. They are so used to people. This weekend there is a special red squirrel weekend organised in formby for the interested people.