I am playing on the All The Mods 6 pack and made a simple setup with a hand-crank-powered encased fan blowing through fire, lava and water in that order. I used depots to keep the items from being blown into the fire while smelting and the game crashes as soon as any itemstack would have been smelted into another stack. I then tried placing iron bars between the fire and lava instead and this also caused a crash at the same time. Maybe the problem has something to do with the fan blowing through multiple blocks which modify the air current.

Is there polymorph and fastfurnace in the pack? Try update the polymorph mod then. Probably a duplicate of #555