To see the full report, printed in the journal Environmental Science & Technology, requires payment, but there is an abstract and Green Car Congress has some more details. The gist is that, "with increasing ethanol content in the fuel, the tailpipe emissions of ethanol, acetaldehyde, formaldehyde, methane, and ammonia increased." At least NOx and NMHC emissions decreased. The researchers say that the effects are due to the fuel and "are expected for all FFVs," but that the way that a manufacturer calibrates the engine will affect NOx, THC, and NMOG emissions.
It's this last bit that's important, since the researchers found, "Higher ethanol content in gasoline affects several fundamental fuel properties that can impact emissions. ... These changes can have positive or negative effects that can depend on engine design, hardware, and control strategy. In addition to direct emissions impacts, higher ethanol content fuel can also provide more efficient combustion and overall engine operation under part-load conditions and under knock-limited higher-load conditions." So, as we head towards more ethanol in our fuel supply (maybe), manufacturers are going to need to learn how to burn it most efficiently.