I am using colour correction, I disabled it but the issue is still there. If I disable depth blend on the water below, the issue goes away. It's only visible when the alpha clip shader overlaps the water.

Edit: looks like I needed to use Light attenuation, but still getting interpolator errors unless I just use a constant in diffuse

yep!

Made a simpler shader just in case it helps.

Turns out I didn't get the effect I was after anyway (lightmaps affecting other things)

would a single-pass for all refraction help with this? (We discussed it briefly a while back for optimisation)

I can reproduce this issue also.

What about adding an option to set Transmissive Color in SF for Lightmaps? Perhaps it could just detect a colour node plugged into the transmission input in the editor and use that?

I rand into this problem a while back and it turned out that it was because Beast only bakes alpha masked shadows for shaders placed in the /Transparent/ Folder. It's a pain in the arse, and i'm not sure if it can be fixed through SF.

One thing that would be nice to add in regards to Lightmapping and SF shaders though is the addition of Transmissive Color. 

More info on this here: http://answers.unity3d.com/questions/49537/can-transparent-textures-be-lightmapped.html?sort=oldest

Just want to chime in and say this sounds like a really good idea! The Phong tessalation sounds interesting also!

Hope this gets fixed soon!