It looks to me like you just want to change your margins from 0.5 to 1.0. You might want to click the "Graph..." button to have a look at your isolation scheme graphically. Also, if you used the "Import..." button to have Skyline calculate your isolation scheme from one of your data files, I would expect the algorithm I wrote to get it right. But, if you did use the "Import..." button, I definitely want to fix that and it would great to have one of your data files to test that with. Though, I am guessing you entered the isolation scheme yourself and just use 0.5 as a margin because that is the most typical value and the one published in the original SWATH paper. Just not what you used, since you can see that your measurement windows actually overlap by 2 m/z.
677.3 to 688.3
686.3 to 697.4
695.4 to 707.4
The right margin here is 1.0. (Though, interesting demonstration of the signal change between windows even with a 0.5 m/z margin applied.)
Thanks for the informative screenshots.