Same problem here too. I have an Industrial Tesla Coil setup to kill mobs around my town and farm ender pearls and gunpowder that happen to drop.
My current programmable filter setup looks like this:
It works fine for the item collection but also zaps and subsequently destroys any items that I did not specify in the loot collector. So basically the same problem you have. What we need is some sort of logic programming that says activate item detection token only if (specify item) is present.
What we need, I think is to tell it that only activate the Item Detector token if certain conditions are met; in my case, activate if gunpowder or ender pearl is present. But alas my other experimental iterations still just zap every item out there.. (including my MFSU T_T)
