When I switch to another windows and back to Minecraft, it sometimes freezes (Javaw.exe doesn't react) for some time. How long this time is, varies, sometimes it doesn't even catch itself anymore and I have to terminate the process.
Not just 16w02a, but also previous 1.9 snapshot and I think even stable versions had this problem. Also on my laptop where I have the new launcher. On both computers there are JVM arguments to give it more RAM.
In the video I have sped up the part where I do other things in another window. It seems like Minecraft doesn't lag when I only switch away and back very quickly.