Im having the same issue....sorta. In whatever state my bike was first titled in, titled the engine instead of the frame. SC doesn't title engines so I was pretty much forced to get an engine title for the bike and I now have to get an antique title which will be a big pain in the terd cutter. I can register my bike all day long, but it really isn't all that legal and whats worse is the DMV allowed it. But whatever its on them.
Here in SC if there is an error on the title that the DMV messed up, they will print you a new title free of charge. I am unsure of your state though.