yes and no.
you might be able to fix the problem by cleaning up the geometry (polygon -> Cleanup, or something like that) - make sure all the normals are correct, usually no 'holes' in faces, that sort of thing. In addition, it can usually be better to do an intersection instead of a difference.
Unfortunately, if neither of these things work..... you may not be able to do anything about it. Maya occasionally just does this, and I'm not sure why (even with 100% compatible hardware, near as I know).