Microsoft's Dan Fernandez has issued a statement apologizing for the company submitting a patent that appeared to copy BlueJ. They have promised to pull the patent submission and investigate what caused it to be filed in the first place. Microsoft has always had a bad image with patent applications, and this is just the latest in a series of bad PR moves. The most recent of which was the RSS Patent Controversy. Nail Kennedy at the time commented that there were some patent worthy inventions in that case, but that the patent as a whole was probably invalid. Nail's summary is also relevant to this latest episode, specifically where he mentions the importance of patents in the Microsoft culture:
"Microsoft employees receive an inscribed granite cube and a financial reward for each patent granted. The trophies are often displayed with pride for any visitor to quickly count. If you possibly invented something you're encouraged to submit a patent to reward yourself and the company."
It's obvious that Microsoft employees are being a little over-zealous on filing for patents.
I wonder if it's a managerial problem personally. How far fetched would it be to believe that employees in some groups have a "patent application goal" that they are to meet? Perhaps they're throwing stuff at the wall for their manager's sake, not really believing any of it will stick (i.e. get past legal).
Regardless, Microsoft has to re-examine it's patent application structure or the bad blood will continue. The developer community is wary of software patents to begin with. For every point Microsoft gains with the developer community for an open standard or some cool technology, it loses two points for every sinister looking patent application.
Kudos for Microsoft for doing the right thing in this case though! Remember, they're like "Blaster" from Mad Max Beyond Thunderdome, not evil, just big and dumb.