I have a feeling this isn't going to help at all
When you create your first brush, make sure you don't turn it into an entity.
You can sometimes get this error by trying to assign an entity to another entity. However you should get a little pop up asking you if you want to assign both solids to the new entity. If you click No, then the old entity will appear non solid and have co-ordinates that are way off the map. This old entity needs deleting.
But there seems to be more to your problem... Post an example of what has happened in the Problem Maps section of the Vault, and someone might be able to shed some light on it.