Thank you for the help!
Wow! This is kind of funny!
1. So I did a quick scroll of this thread to make a screen shot to post to demonstrate the "red lines." I used automatic scrolling (SC tried a few methods and selected one) instead of manual. Then I used the automatic margins and automatic overlap. I have not inspected the result thoroughly, but it appears that it came out PERFECTLY ... both margins AND overlap. In addition, for the first time ever for me, the scroll only contained the browser window, not the Firefox page tabs or command menu etc. above the browser window. That is what I wanted to achieve but I don't have any idea why it did that this time and not the other times. Weird. I'm going to have to experiment with that to see if I can figure out what's going on.
2. The red lines are not related to SC! As I was doing this I finally realized what they are. I run Firefox in a sandbox. The sandbox puts lines around the Firefox window. But the way I have it set up they are barely visible and I am so used to them I forgot they are even there.
Now... when you use the SC editing window for setting margins and overlaps, you can see the red lines around each slide. Just coincidentally, they appear in the perfect place around each captured slide because they surround the captured window. So all along I assumed these lines were part of SC... there to help you adjust things so you could easily see the edges of each individual slide! Actually, I thought that was a very useful feature! The lines are red and partially transparent.... perfect for seeing where the edges are with precision as you adjust them!
So I assumed those lines were part of SC. I didn't realize they were actually part of the capture!
This has to be one of the oddest things I have ever seen when testing something like this.
But honestly, I think the semi-transparent red lines around the slides in the stitching dialog are a very useful feature... maybe something you might want to consider! ... of course they shouldn't appear on the output.
Bottom line.... the red lines are my mistake.
But maybe not a bad idea!
I attached the slide of the output image anyway to show you what I mean. As you can see, the red lines appear at the end of each break. It was even useful having them in the output because it allowed me to inspect the overlaps quickly as I could see where the page breaks were. But of course, except for testing purposes, I wouldn't want them in the output... only in the editing dialog. On further inspection it appears that the "internal" overlaps look perfect! ... and those are the ones I had problems with. The last page is off, but that's not an issue. But how everything worked automatically this time and not the other times, and how this time it only captured the browser window and not the application window is still a mystery to me.
But pretty cool!
Try as I may I have not been able to reproduce the scrolling capture of just the browser window that I did once and now can't repeat. No matter what I do, every scrolling capture I do now includes the entire Firefox application and not just the Firefox browser window. I even tried it out of the sandbox but got the same results.
Here is what I am doing:
1. Ctrl+Shift+PrtScr ... The Red SC dialog appears in the upper left of Firefox.
2. From the "gear" icon on the left of that dialog I select "Capture Selection Now"
Except for the one time I did it, when only the browser window of the Firefox application window was captured, the entire Firefox application window is captured every time. So each separate frame includes not only the browser window but the entire Firefox application screenshot. I don't know what made the difference.
Is there any way to select which window is captured on the scroll to intentionally select only the window that scrolls?