Curviloft has a low tolerance for messy operations and it won't work around geometry it sees as invalid. I've found that the key with Curviloft is to try and keep your operations in smaller grouped sections and don't try to get complex shapes in one big pass. Once you have each section worked out, then you can explode the groups if needed.
Curviloft is great, but you have to do things nice and clean. Ramming together lots of elements with irregular spacing or breaks you will give you problems. It's also a good idea to use Curvilizard to weld your splines together when necessary.
And be sure to save inbetween each successfully lofted piece.
