I don't know what exactly your issue it, but to avoid numerical problems associated with positive definitness of the covariacne matrix, Cholesky decompsition may be used.
As addition to the previous advice I can recommend Bierman Factorization, which is very popular in practical applications of Kalman Filtering in the INS/GPS Integrated Systems. You can find all details in the book: G.J. Bierman. Factorization Methods for Discrete Sequential Estimation. Academic Press, 1977.-241p.