Hi psytech, welcome to the site and i apologize for the delayed reply.
Capturing a scrolling window is tricky stuff and sometimes the program can get fooled. It's normal for it to scroll back up and repeat down again as it tries to scroll horizontally.
I've been meaning to revisit the scrolling capture code for a while now and try to make it more compliant with some of the recent changes to browsers.
However, one thing i always suggest is that for people who frequently need to capture large pages from browsers, there are some specific tools and plugins for this particular specific job, that are probably better suited to the task.
For firefox there are some good free plugins. I'm not sure if there are good plugins for IE but there is
iecapt, a free standalone utility to capture a large web page.
Having said that, i will try to improve the scrolling capture in Screenshot Captor.
Can I ask for a sample online url where the stuttering effect happens reliably?