I seem to have the same problem with new update (intel XDK 3240). Everything was working fine on build 2893 with CLI 5.1.1.
I also get "app not installed" problem when I try to install the apk on my nexus 5 6.0.1.
Have you been able to fix the issue olkina?
Edit: I goofed up...I realized I had a previous version installed. Uninstalling it simply fixes the problem