The method is almost certainly different; capture works very well for some pages, less well for others. You could try printing the webpage (or better the Reader View) to DEVONthink (so in Safari do ⇧⌘R and then ⌘P and select PDF/Save to DEVONthink 3). If that works for you, you can add a shortcut to the last step, so that ⇧⌘R ⌘P ⌘P would work)