There's an inaccuracy in the article, Microsoft didn't think they were dealing with AST, they were dealing with AST. From the press release he links to:
"The patents were recently purchased by Allied Security Trust (AST) from Microsoft to ensure the patents did not fall into the hands of non-practicing entities (more information on non-practicing entities is available at http://en.wikipedia.org/wiki/Patent_troll, among other sites) that could seek to assert the patents against Linux products."
"The patents were recently purchased by Allied Security Trust (AST) from Microsoft to ensure the patents did not fall into the hands of non-practicing entities (more information on non-practicing entities is available at http://en.wikipedia.org/wiki/Patent_troll, among other sites) that could seek to assert the patents against Linux products."