When I remove an scaffold, doubles the item, (furthermore the wiki say tree wooden planks and tree sticks make 16 scaffolds), as well the universal fluid cell... and I don't know it's intended but, the extractor don't take up rubber wood.
And I feel stupid asking this but, if had a wrench and I cilck on a macerator and an ore washing plant, shouldn't give me the processors insted a machine casing? 
Thanks for your hard and lovely work 
Items Duplication And Extractor
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Yeah the wrench is supposed to work as you said, give the machine itself not the casing. Are you using the 1.8.9 version?
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yep
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I use the 1.8.9 version
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Regarding the wrench: the wrench has a chance of dropping a machine casing instead, if it's not an electric wrench on lossless mode.
The extractor not taking rubber wood was fixed, so just update your IC2.
What do you mean with scaffolding duplicating items and that it should give you 16? -
The wooden scaffolding recipe hasn't given 16 in years, ever since Greg nerfed it.
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Note that I nerfed it because they were UBER Fuel in the Furnace, much better than Charcoal, due to the limit on how low a Block made of Wood can have its Burn Value.