I have never seen this bug before but my character's eyes have started to glow like searchlights for no apparent reason. Also no one is blinking. It also seems that all of the problems other patches fixed were broken by 1.9, and I have reset the patch twice on my xbox after clearing the cache. It is still broken. Any ideas?

It is broken. Patch 1.9 introduced some new glitches. The never blinking eyes problem you mention, the bad lip sync problem, some npc's sleep with their eyes open, the cave bear pelt was exchanged for the bear pelt (black for brown) on your items inventory, and some more I can't remember right now along with ones I'm sure I haven't yet discovered. There is no solution for that. There are still many more glitches, like the bad respawns and much more others, and sadly, it looks like Bethesda won't be fixing any of them now that they are done with Skyrim and about to release the Legendary Edition.

Of course, Skyrim is like old skin, and BGS has shed it to let it fall off and rot.