Members of our Users Group have often warned each other to never directly import a Gedcom into our main project. The best thing to do is to start a new project, import the gedcom, look it over and work with it. THEN (and only if it is as you want it), you can combine the projects.
For now, however, you might be better off reinstallig the project USING THE CUSTOM OPTION (so you won't lose any data). Someone else may have a better idea, however.