I know the last reply here was 3 years ago, but I had the same problem recently, and I also think the issue is Skyrim loading too fast. My solution has been to have a video running in chrome (something on youtube for example) while starting skse. This seems to slow down the processor enough to consistently run the injector properly. Once Skyrim is running, you can close out the video to reclaim your processor power.
My guess is that it doesn't necessarily need to be a video, it could be simply having several browser tabs open, you just need to bog down your processor a little when starting skse.
