Oh do you have some items dropping when others should? If so from what I know the only thing you can do is find out the items ID using NEI then fin dout if there is another mod using that id by going through configs. I actually have been trying to find a program to help with this but so far. No luck.
I am using the beta 152 wgt with a couple additional mods. I think I fixed all of the conflicts, but I'll never know until I run across it in survival. Mostly, the problems I have had so far are with Ars Magica.