I think there are now more files that need to be marked executable:
nw (or whatever the main file with the name of your project is)
nacl_helper
nacl_helper_bootstrap
anything ending in .so
If those are all marked executable the NW.js app should start up.
It's a bit tricky given C2 exports on Windows which doesn't handle UNIX file permissions :-\ We should probably make a bash script to do that...