When I try to use Spectacle on Omnifocus or Omnigraffle, spectacle is not able to complete the "Next Third" or the "Previous Third" but can complete the corner commands.
Some apps restrict the dimensions of their windows. In this situation Spectacle will encounter trouble. Unfortunately it appears that these apps fall into this category.
In Omnifocus, at least, I think the reason this happens is because the min width of the window is greater than the size you are trying to fit it into. The sidebar and inspector add to the minimum width. I contacted omnifocus help and they pointed out that if you disable both, you can get the bare list to fit anywhere. I also have problems with the 1/2 view not aligning properly. What works & what won't will depend on the horizontal resolution of your screen.