I'm just positive it's the patch that fucked it up for me, as it worked before I downloaded the new patch :/.
No worries, I read your first post.
When I look at your Window Layout it seems to be apparent why it doesn't use your full second screen. In the preview of your Window Layout, the screens are not even touching. I would guess that the layout on your actual monitors looks a lot like it does in your Window Layout. To see what I'm looking at, go into the top left pane under Window Layouts and select yours; then in the bottom left pane, click on "Regions". According to this, you have one 1920x1080 monitor, and one 1536x864 monitor. However, the second monitor is actually offset as though the monitor is really 1920x1080. So my guess is that it is using 1536x864 of your 1920x1080 monitor. And this isn't from the Inner Space patch, it's just applying your Window Layout...
So assuming your monitor is 1920x1080 and not 1536x864, and assuming that you're not manually editing it during the Window Layout Wizard to make it think it's 1536x864 ... you want to set the Windows 8 font scaling setting to 100%, it is apparently set at 125% (actually fairly common for high DPI displays) and for some reason this makes Windows report the monitor size incorrectly. After you set that, use ISBoxer's Window Layout Wizard to replace your current Window Layout. You can probably set it back to 125% after you Export to Inner Space. To find the font scaling setting, mouse to the upper right corner and click Search, then in the search box put in "dpi" and click the "Settings" category right under it. Click "Make text and other items larger or smaller", and set it to 100% there.
I'll see if I can find out how to get around this on my end...