If you want to transmute something on the highest area of the philosopher stone, the game crashes. I took the crash report and put it on pastebin for you all: http://pastebin.com/StgYWJaE
If you need anything more, just comment and I will post it.

The philosopher's stone isn't meant to be totally usable at the moment. That's one of the reasons it doesn't have a crafting recipe yet.

I guess your right... I would like to see it working though :)

Fixed in Forge 727 and higher - just update your Forge to Latest and you should be fine. Also, the Philosophers Stone isn't done, so reporting bugs on it is pretty useless at the moment.