I'm having the same problem. I just gave this a try again in v1.0.4.0540 on linux and it still seems to be broken.
Here is a screenshot of the issue http://mindkeep.org/public/Screenshot_2015-03-28_13-16-47.png. Right is my primary monitor in landscape and the left monitor is secondary in portrait (rotated left). nvidia presents this to X as one massive monitor with dead zones in the upper and lower right. If I disable the left monitor, everything works fine, but it's annoying to have to switch between the 2 modes.
Option "metamodes" "DVI-I-1: 1920x1080_144 +1050+270, DVI-D-0: 1680x1050_60 +0+0 {rotation=left}; DVI-I-1: 1920x1080_144 +0+0; DVI-I-1: nvidia-auto-select +0+0"
This let's me swap via "xrandr -s 0" and "xrandr -s 1" to enable/disable the left monitor.
Most games will work just fine in full screen mode, which will use ony the primary (right) monitor, allowing me to keep some reference page vibily on the left/portrait monitor. It would be nice to see this fixed.