Connecting DDR3 Controller to Chip Pins

You should be able to hook them up directly, i.e. no buffer or anything in between. Regenerate your megafunction and have it generate an example design(it asks after you hit finish the megawizard and click generate). That will create a full project with the DDR3 core instantiated and hooked up to I/O(as well as a pattern generator that tests it). Just look at that example and see what's different.