Hello!
I'm currently running Unity 4.3.4f1 (I do plan to update Unity later, after squaring the following away!) and just updated 2dtk from 2.3.3 to 2.5.4. After this transition, all of my sprites from my existing SpriteCollections look pink. If I change a SpriteCollection's shader from the standard tk2d/BlendVertexColor (which used to work for me) to something like sprites/default, the sprites show up in my game view but have some weird display errors and are still pink in editors like the SpriteAnimation editor. I imagine there's an easy fix for this, but it's eluding me so far.
Along the same lines, I tried to create a new SpriteCollection and am running into a similar issue. The resulting sprites look pink, and by default the created material isn't even connected to the created atlas. A lot of the new settings go over my head, but prior to updating, this approach worked -- so I was able to get away with my lack of knowledge by default!
If you need any more info to diagnose, just let me know.
Thanks for your help!