I can't think of any reason why it should be giving you trouble like that.. Screenshot Captor was made to work well with multi-monitor setups.
Let's see if we can pinpoint the problem a bit more.
If you try other capture modes, most notably the "capture entire workspace" mode, does it capture all monitors as one image, like it should?
When you say the screens go black, can you elaborate. Do you mean the screens go black and the crosshairs appear on the black screen until you select a region, and then when you select a region with the crosshairs.. what happens? does it capture black or the correct area of the invisible black screen or?