I had the same symptoms you described MBlazerGuy. If you're still having issues, try messing with the Anti-aliasing settings on KSP. I have found that both 2x and 8x cause the 1920x540 issue whereas ShadowPlay records correctly after turning off Anti-aliasing or using 4x. ShadowPlay has such huge potential. I just need to keep reminding myself that it's a beta and while there are still bugs, it can only get better from here. Good luck with your setup!