I was about to post this same problem; however, I think I know the issue.
I use Nova Launcher and tried adding a bookmark from Dolphin; however, it says it would be added to homescreen but when I look, nothing is there. I would try to add the same bookmark again; however, it would say that the bookmark/shortcut alread exists.
At first, I thought that it was an issue with the browser itself; however, I had a hunch and removed the defaults from Nova so that I would have to select between TouchWiz and Nova when I pressed the home button.
It turns out that those shortcuts are somehow ending up in the TouchWiz launcher even though it is not selected as the default.
I tested this out using Chrome and I had the same issue, which is how I concluded that the issue was not with the browser itself.
Currently, the only workaround that I have (which works with Chrome only) is to (in Nova Launcher) long-press the homescreen to bring up the menu, select "shortcuts" then "bookmark."
