seesmic windowsLoic Le Meur, founder and chief executive of Seesmic, demonstrated a new Windows version of Seesmic’s desktop console for managing your alerts and accounts in Twitter and Facebook today at Microsoft’s Professional Developers Conference in Los Angeles. After the presentation, Le Meur told me this is part of a big bet that Seesmic is making on Microsoft and Windows.

The current version of Seesmic Desktop is built on Adobe’s AIR technology, which allows applications to run on the desktop while accessing the web, and has the advantage of running on Windows, Mac, and Linux computers. Seesmic Desktop has already been downloaded three million times, but Le Meur said, “We hit limits on AIR.”

His biggest complaint was that Seesmic wasn’t able to plug other services and applications into Seesmic Desktop, the way it has with Tweetmeme and MrTweet on its web version. Le Meur said his big vision is for Seesmic itself to become a platform for third-party applications itself, the way Twitter and Facebook are now, and AIR wouldn’t allow that to happen.

Le Meur showed me some other cool features that he said could only be achieved by building a native Windows application, including a drag-and-drop interface for building Twitter lists, and a transparent background so users can see their computer desktop under the Seesmic app. There is a big missing piece right now: The Windows version lacks Facebook support, but Le Meur said that’s coming in the next couple weeks, as well as an official launch version.

As for Mac and Linux users, well, Le Meur said there are fewer than you’d think — 80 percent of Seesmic Desktop users are on Windows. Seesmic is also developing an application using Microsoft’s Silverlight technology (a competitor to Adobe AIR and Flash), which works on Mac and Linux, but also allows Seesmic to use much of the same code as in its Windows version, making it more feasible for the company to support two different versions. Le Meur said that once the Silverlight app is finished, he hopes to abandon AIR, though that depends to some extent on user feedback.

Le Meur added that moving to Microsoft makes Seesmic unique compared to other Twitter and Facebook desktop apps, which are mostly built on AIR.

“This should get us out of any feature wars,” he said.

Le Meur also blogged about the move.