Aaagogo

Hey guys, have a weird problem that I can't seem to solve. I am building/running a custom printer, Marlin firmware with a Megatronics V2.0 Board When I connect the printer to Cura 3.6.4 directly via USB, the printer does not work, and the hot-ends does not show temperature and the controls, both g-code and home buttons in the Monitor tab does not work. However, the printer works fine when i run Cura 15.04.6, Slic3R 1.3.0 and Repetier Host 2.1.3 both directly connected via USB. The printer also works fine when i print with Octoprint via Cura 3.6.4 would anyone be able to shed any light on what might be the possible issue? Cheers