Currently the xsettings plugin sets the subpixel order while the xrandr plugin handles the screen rotation stuff.  The problem is that when the screen is rotated, the subpixel order needs to be updated to accommodate that.  For example, when the screen on a RGB-ordered laptop is rotated left, the screen will have a VRGB order as far as the applications (cairo in this case) is concerned.  It would be rad if gsd can automatically send an update for this.  Currently there is no solution short of the user manually changing the subpixel order.