This paper reports the effects of nozzle exit boundary layer swirl on the instability modes of underexpanded supersonic jets emerging from plane rectangular nozzles. The effects of boundary layer swirl at the nozzle exit on thrust and mixing of supersonic rectangular jets are also considered. The previous study was performed with a 30°boundary layer swirl (S=0.41) in a plane rectangular nozzle exit. At this study, a 45°boundary layer swirl (S=1.0) is applied in a plane rectangular nozzle exit. A three-dimensional unsteady compressible Reynolds-Averaged Navier-Stokes code with Baldwin-Lomax and Chiens $kappa$-$xi$ two-equation turbulence models was used for numerical simulation. A shock adaptive grid system was applied to enhance shock resolution. The nozzle aspect ratio used in this study was 5.0, and the fully-expanded jet Mach number was 1.526. The "flapping" and "pumping" oscillations were observed in the jets small dimension at frequencies of about 3,900Hz and 7,800Hz, respectively. In the jets large dimension, "spanwise" oscillations at the same frequency as the small dimensions "flapping" oscillations were captured. As reported before with a 30°nozzle exit boundary layer swirl, the induction of 45°swirl to the nozzle exit boundary layer also strongly enhances jet mixing with the reduction of thrust by 10%.