Okay, I will have a look.
You may be interested in this issue I posted in response to your confusion:
In working on the isolation scheme editor, we eventually concluded that there were two different "windows" involved in setting up an isolation scheme:
1. The instrument isolation window, or the range you actually set the instrument to isolate
2. The extraction window, or the range from which you want Skyline to extract ion chromatograms
My initial design for the feature was to use #1 as the only think shown to the user, since I expected people like you to be using the feature, arriving with an existing instrument method.
However, in working on the feature, it became clear that this was also confusing to people, and it was actually clearer to people that they had contiguous non-overlapping extraction ranges, when that was expressed in the ranges displayed in the grid. So, we decided to switch to displaying #2.
Now I am willing to try figuring out a way to offer to display either way. Hopefully that will make it clearer.
We also had in mind some kind of graphical display, but never quite got to that.
Thanks for posting your data. Hope that helps to clarify a little.