I have disabled system integrity protection on El Cap following this Ask Different question but it keeps coming back every time I reboot which is annoying. Is there an extra step I need to perform to stop SIP switching itself back on after reboot?
There should be no extra step required - in fact, reading through the excellent article linked from that question, I found this…
Because SIP’s configuration is stored in NVRAM, SIP’s protection settings will apply to the entire machine and will persist even if the OS is reinstalled.
This would perhaps imply your NVRAM is not correctly holding data -
perhaps try a reset, Cmd ⌘ Opt ⌥ P R at the chimes & keep holding until you hear the chimes a second time.