I haven’t tried V2 but I know that the latest V1 versions work with the latest NDK and I have no issues with them.
Also, I thought you had already managed to build your apps but have issues in them, are you sure it's the templates that's the issue.
You could try setting up everything on linux instead, that was a lot easier for me because you didn't have to go thru the cygwin steps and I think I was able to get my enviroment setup in 2 hours or so.
Say ONE stupid thing and it ends up as a forum signature forever. - Neuro Fuzzy