Yesterday we discovered an issue with the Select All checkbox that is available in the Project Settings --> Plugins section of the XDK, build 1878. What actually happens when you check this box is that each plugins files are being copied to your apps project folder, into a 'plugins' folder.
The issue is that if your check the box, and then leave the Projects tab before the copy is complete (my machine took 45 seconds), the copy just stops, yet all the plugins are selected. This is causing issues and with testing apps in App Preview as well as builds. We are working on implementing a solution and will provide an update ASAP.