Software Patents - the Lunacy continues

I believe in software patents. I believe that the time and energy invested by people to solve a problem should not be subject to theft by others without fair compensation. Still, this story leaves me a bit unnerved.

My opinion is that, if I am working to solve a problem, and am unaware that someone else has already solved the problem and patented the solution, I should not have to pay this person for his solution, even if I come up with a similar one. As long as I can show that my research was "pure" (i.e. not influenced in any way by the other person's solution), I don't think I should have to fork out money twice to solve the problem.

In the case above, I find it hard to believe that Microsoft was unaware of the patent. After all, when a big company like Microsoft develops new products, I'd imagine they have a team of researchers out there trying to determine whether someone else already has patent rights.

Ironically, the patent holder in this case is working on another research project called Dark Iron (insert copyright symbol here - I don't know how) that sounds suspiciously like a common worm / distributed attack software. I wonder whether the American Hacker Alliance (AHA) will be filing a patent-infringement case against Mr. Doyle?