Edo -- those two numbers do not make sense. It looks to me like one is a Crosswalk build and one is not. To check that theory, unzip each into separate folders (an APK file is a ZIP file) and see what's inside the "lib" folder in the unzipped output. If you see Crosswalk libraries in one, but not the other, my theory is correct. If not, something else is going on.
Did you want to build for Crosswalk?
p.s. I've also changed the title of this post to be more descriptive of the issue.
Edo -- I've confirmed that there is a problem with the exported config.xml file that is adding in the Crosswalk plugin, regardless of the state of the Crosswalk optimization choice in your Build Settings. See this thread for more details > https://software.intel.com/en-us/forums/intel-xdk/topic/720917 < I'm closing this thread and in favor of that other thread.