In general, when using third party shaders, please contact the respective developer for help.
edit: Sorry, just saw your other post here Shadero Sprite and Spine and that you have already asked Todd River, without any reply.
I have tried Todd River's Uber Sprite shader on our Basic Platformer sample scene: It worked very well unless I enabled "write to depth" at the material and at the same time set "Z Spacing" to larger values, which causes the effect you described - eyes will write to the depth buffer and therefore cast shadows onto the face. So I suggest that you either reduce "Z Spacing" to as close to 0 as possible, or disable "write to depth".
As a side note - you can achive the same results with Spine's Sprite shaders, e.g. "Spine/Sprite/Pixel Lit". If you are missing some crucial functionality there, please let us know!

Since I would be happy to improve the Spine shaders or add new shader features, please let me know what you are currently missing from them - we would be very happy to provide everything in the Spine shaders and eliminate the need for any other shaders!