The mouse cursor is offset along the vertical. It seems as if the mouse position is scaled, so that the game thinks the mouse position is higher up than it is. The difference increases the farther down on the screen you get. My screen is running at 1920x1200, Rift is running at 1920x1200 fullscreen, and my ISBoxer window layout is set with all regions on top of each other at [0,0] to [1920,1200]. I have 3 characters running on one PC and 2 characters on a second PC. I only have this problem on the main PC, not the 2nd. All five characters are using the same ISBoxer window layout. Both PCs run at the same resolution.
The problems means that to be able to click on an in-game button, I have to click a bit further down on the screen than where the button is. It also means that repeating mouse movement and mouse clicks is impossible.
If I set the in-game resolution to 1920x1160, the mouse cursor will line up fairly well with the mouse positions sent to the game. If I set the in-game resolution to 1920x1080, the mouse cursor will be scaled upwards instead and won't match with the in-game UI anymore. It could also be that it's not a scaling issue and it's just offset by the Windows taskbar size and I'm just imagining that it's a problem with vertical resolution mismatch... If I run the game normally without ISBoxer, the mouse cursor will line up just fine with my normal in-game resolution at 1920x1200.