Ok thanks. To reproduce on my end I simply publish my files to Unity Collaborate, then I double click a shadero project. When I drag my shader asset onto the build shader I get the corrupted display and the spammed output saying that I am pushing more GUIClips than I am popping. I am on v1.9.
I use Texture Atlas to regroup my sprites on one texture, but it's not a animation spreed sheet, I don't have sprites animations. Texture Atlas is generated differently each time I add a new sprite, to optimise and minimize texture size, and so the memory usage at runtime, and to use draw batches.
Animation spreed sheet have the particularity to be "sorted" by frame order. Not a "classic" Atlas Storage
I have only one big optimized texture 2048*2048 with my sprites disordered
After some searches, it is possible to filter the pixels in the shaders, by passing sprites coordinates by code, but the shaders code should be changed to receive coordinates. Not convenient
So I choose to create a texture copy by code for a sprite rect when shader is needed, add it in a cache for reuse. It adds a little more memory of course, but it works well with a generated atlas
I will add a request for evolution to Unity
The blend mode initialisation is an issue and it's should be fixed in the next release.
The loading project part is truly something that need to be improved for the version 2.x
Thanks for reporting thoses issue
I just finish to optimize my current in-development game, I suggest you a good reading to start : http://www.theappguruz.com/blog/learn-draw-call-reduction-and-make-your-games-run-superfast