Recently the multi-planet system OGLE-06-109L has been discovered, where the two planets show similarities with the Jupiter-Saturn configuration of our Solar System. The orbital parameters of this new system indicate a high inclination for the outer planet. In this parameter study we show the stability of the two planets for different relative inclinations and semi-major axes of the two planets. Using the errors in semi-major axes given by the observations, the best result concerning dynamical stability has been obtained when planet b is at 2.1 AU and planet c at 5.1 AU. The worst result has been found for the closest configuration, when planet b is at 2.5 AU and planet c at 4.1 AU. The second part of this study examines the stability of test planets in the so-called habitable zone (HZ). This is the region around a star where liquid water is stable on the surface of an Earth-like planet. The stability of test-planets in the HZ is shown for different relative inclinations (up to 50°) of the two giant planets in OGLE-06-109L system and then compared to the results of a similar study in the Jupiter-Saturn system. For high relative inclinations we observe strong perturbations in the HZ in both results, which is probably caused by the Kozai resonance. In the OGLE-06-109L system we also observe secular perturbations for low inclinations around 0.3 AU. For certain mutual inclinations of the two giant planets we have found nearly circular planetary motion in the HZ.