If any one is still interested or comes across this thread. I had the exact same issue with my NVIDIA GeForce 650M card. Here is how I got ENB Injector and SKSE to work with Mod Organizer. First setup ENB Injector as an executable within Mod Organizer. Just like you would do with SKSE. Each time you start you game you will need to launch ENB Injector, minimize it to tray, then "unlock" MO and then launch SKSE. I tried various .bat files and arguments within MO, however this procedure was the only way I could get MO to recognize the ENB Injector along with SKSE.