I have purchased software that scrolling capture doesn't work on, unfortunately I can't provide a test as having the software would not help, you'd need to connect to my company's server before you'd have a window you can scroll. :-(
If my observations are correct, SC is unable to determine the size of the window to capture. The window flashes several times but does not scroll as I'm used to seeing. The actual capture is a single screen from somewhere a few lines down from the top of the window.
I don't see evidence that SC is troubled by inteference, such as from scrollbars. Nonetheless I tried the advanced options such as sendkeys, with and without large ignore margins. These tests have not made a difference, as they appear to only affect the process of the actual capture and not what comes before.
If you have a debug/logging version, I can run that for you. I can also send you a video of the desktop while SC is attempting the scrolling capture. Please let me know if these would help, or if there is anything else I can do to help resolve this issue.