Hello,
Seems NesDS runs in fullscreen on the DSlite by looking at some videos on youtube. In the video you can see him select "Display" settings which is where the above post is referring to.
http://www.youtube.com/watch?v=k2Kap9Y8jc0
That being said it could possibly just be a compatibility issue.
Suggestion to update firmware and operating system to latest versions and make sure you are running the latest files
Otherwise if you are running the latest, it could just be down to the software itself.