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As you noticed, you have to escape the parentheses. A good browser will do that for you... (this has been reported many times - Brandon illustrated another way of getting the link to work in his edit) – Shog9 Oct 13 '09 at 19:48
This is a known issue. You can take a look at these two questions for more details on linking on SO.… and… – Brandon Oct 13 '09 at 19:49

This is essentially by design; have you read the markdown help?

There are at least 5 different ways to make links
<a href="">foo</a>

and of course the default toolbar markdown (footer-y) way

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