The ones you bought on eBay are likely "unlocked". Companies buy "used" FOBIKS and put new shells/button pad/key blade on them, and basically flash them to be virgin chips (No longer married to a different vehicle), and sell them cheap.
Contact the eBay seller and notify them of this, and have the dealer put that on paper for you that they can't program the remote part. When I use my equipment to program these, it programs the remote portion automatically at the same time so i'm not sure whats going on.
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2008 335i Twin-Turbo