I cant say I have ever heard of this but anything is possible. Another option may be to make or have someone make you a adapter plate, you could gasket both sides and use longer studs. I really wish this site would take pictures because I'd love to see what this looks like, I am having a hard time visualizing what you are saying. Obviously the mounting tabs/holes are lining up, so in my mind what you are saying is that the port on the manifold does not cover the port on the head. This would suggest to me perhaps bad casting as you suggest - you didn't say but I suspect they were used, so that means they probably didn't have this issue from the factory, meaning that whatever they were on they fit. So, that means that the heads you have are different.