If the package.json is correct then this probably has nothing to do with c2. Which version of nw are you using? r190 installer uses 0.11.1 - but you can easily revert to 0.10.5 (much better IMO) by following this guide
Try the old version and see if your problems are fixed. If they are, then it's definitely a bug with the new version of nw - they can only fix it if you report it to them. Does this happen with both x86 and x64 exports? Are you making any requests to the browser object / nw object?
As far as I understand nw wrapper - if c2 sets the boolean correctly then this is probably not a c2 bug....