Some structures spawn in with lit furnaces and this mod doesn't replaces them with cobblestone.

Lit furnaces have been added to the list of blocks to be replaced with cobblestone in 1.4.6.

That being said, if you still have difficulty with this feature not replacing blocks that you think it should, I recommend you use a tool specifically designed to remove or replace blocks -- a tool like OreStages or WorldGen Block Replacer.

The crafting table and furnace replacement features were designed to replace the blocks generated in vanilla villages because it was required to support the zero-configuration, Pyrotech + Vanilla only experience oriented design. It was never meant to replace blocks added by other mods.