I updated to 10.11.4 and i didn't install dark boot this time and its been showing as SIP off for the past 3 days, so i think dark boot is whats causing the bug.
There have been ample reports: https://github.com/w0lfschild/DarkBoot/issues. That program makes changes to the boot loader configuration. Did you install this every time after re-installing OS X? I would have expected that files of that kind are overwritten by a complete system install.