There must be something about your geometry that these algorithms don't like -- they aren't perfectly robust, but are generally pretty good.
Without knowing your geometry, we can't really make suggestions as to how to fix it.
You might try deleting components (say 1/2 at a time) to try to narrow down what is causing the problem.
In general, I recommend people start with simple models, building up the complexity gradually. Similarly, if your intent is to run VSPAERO, start simple, checking how VSPAERO does each step of the way.
Rob