Not sure why it started happening but I now get double images in the Vive and in the desktop window. I was playing around with custom resolutions but I dont think that causes the problem. I uninstalled Flyinside, deleted the prepar3d_FlyInside.cfg and all files in Appdata\Roaming\Flyinside before reinstalling. Still have the same problem.
Attached is a picture of the desktop window. This is the same image I see in each eye of the Vive. The ViveHome test image works okay.