Yeah we figured it out.
flying_hamster was using a perspective camera for the tilemap, had multiple layers and was running on Unity 3.5.3/2D Toolkit 1.7. In that version of 2D Toolkit, there was a workaround for a Unity 3.4 - 3.5.2 bug to do with inertia calculation. The workaround was, one of the vertices per sprite was pushed back slightly.
When viewed with a perspective camera, occasionally (well quite often) the parallax from this slightly offset vertex would cause the pixel behind to be visible. Sometimes this was dark.
If you're using v1.75/6 and Unity 3.5.3 then this should not be a problem any more - just in case, re-commit your sprite collection and see if that improves anything. If not, it could be something different... in that case, a repro project would be very much appreciated.
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