Ok, so i think i have an inkling of the issue -- so it's related to how your monitors are laid out, it must be confusing SC.
I think we can call this a bug, and i think i can fix it.
Can you test something for me -- can you try Grab Entire Workspace (Ctrl+Prtsc) and see what the resulting image looks like (maybe post it as an attachment). I'm interested in seeing if it gets the layout of all monitors correct. Because of your layout, there should be some big white areas in the resulting rectangular image...