What is connected to the ender chest? If it is a sorting machine then you can either put it in a mode that pulls only what you tell it to from the various columns on the sorting machine or, if I remember correctly, use the mode that pulls anything no matter what it is.
If you have multiple mods than have the same ore gen i.e copper, tin silver etc then you can either turn off those mods in their respective config files or use the pull anything mode from the sorting machine.
If you put the sorting machine in pull any mode the machines you have for processing will process the ores into their respective ingots whether it be thermal expansion, ic2, factorization.
Hope this helps.