Make sure you did a clean save before doing that update. That sounds like the issue that was corrected in 0.9.9.5 and the subsequent fixpack. If it's still an issue, please report it in the official thread where Wrinklyninja is most likely to see it.
Yeah I did do a clean save, I was having trouble doing that at first thought because it was crashing on loading every time I loaded my save and it was you who told me about leaving the real lights.esp active and trying it that way (on the official thread if you remember) and that worked but now this has happened, but if it's something that was supposed to of been fixed then maybe it's just isolated to me so if there's no ideas on resolving it I'll report it over there.