I came across this strange thing today, apparently when when light cookies are set, transparent objects that overlap themselves (so not regular transparent objects) behave weirdly as seen in the image.
I have tried a lot of things but it seems the only thing that fixes it is disabling pixel lighting (aka both forward and deferred) in either a new shader or per light, unfortunately I need this as I want to have a normal map on my transparent objects.
Any ideas would be greatly appreciated, Here is also a link to a stripped down project that shows the basic issue. :
https://dl.dropbox.com/s/6awohhm3jrh31vz/LightCookieExample.unitypackage?dl=1