Item IDs not showing up in config (2 configs being generated)

[cublikefoot]

The config file for Extra Bees 1.4.0.16 (Using Forge 4.2.5.307) is not generating all the item ID's it needs to. There are also 3 config files being generated, one in the "forestry" folder and then two others being generated in the "extrabees" folder in the "forestry" folder, although the latter two config files do not contain anything.