We need more details about your model and, as Nils asked, by providing the matrices we can help you more properly. Meanwhile, I'd recommend you to have a look at the following book, that presents 3 chapters about eigenvalue problems and computational methods for eigensolution:
Computational Methods in Structural Dynamics - by L. Meirovitch
if you are solving a problem in elastodynamics, the matrices, mass: [M] and stiffness: [K] must be symmetric positive definite. So the natural frequencies must be positive REGARDLESS of the element type you are using. If this were not the case, there must be something wrong in your evaluation of the matrices. I advise you to check the SPD property of the matrices before you do anything!
What is the problem you are solving , maybe having a complex eigenvalues is physical! Please identify the problem you are solving to us to better help you.
You need to check first for positive defectiveness of mass matrix and stiffness matrix. If both are positive definitive than natural frequency must be positive real value.
Its same as 4 noded iso-parametric formulation. You have to keep the the order of the shape functions and the corresponding nodes same. They should not differ.