Heres the report for a non-battleye launch. I can confirm that after it has loaded into the main menu, where it shows active addons, there is 2 of both CBA_A3 and ALiVE. The main menu does have very low FPS however; around 4fps.
https://www.dropbox.com/s/rq5uc93d2kbosjl/Arma3_x64_2017-06-27_15-05-17.rpt?dl=0

In task manager, during start up of arma 3, it is using in excess of 15gb of memory...

EDIT: When I remove the command line to load these mods in the parameters, one version of each is loaded which fixes the duplicate problem... -_- BUT now I have really low FPS when in game - around 4FPS.