Windows 8.1 introduces some "features" to accommodate mixing and matching high resolution displays with other displays. However, these new features may break SaT. If you are trying to include a site, and getting a "Button detected as black" message, or if tables are not going to the stack, then this could be an indication of these problems.
There is a setting you need to change in the Control Panel. You need to turn on this checkbox: "Let me choose one scaling level for all displays".
See this video (1m22s):
After you turn that setting on, you will notice that the size of everything on your desktop will have changed. You will want to tweak the scaling % setting to something comfortable for you. You may also need to adjust the brightness and such from the buttons on your monitor.
Finally, you should remove and re-Include all of your sites that you are having problems with and re-test.