When you double click on something in the defs window, it does a push-tag, so it records the place where the cursor is before jumping to the definition. That mark shows the saved position. If you press Ctrl-, to pop-tag, you'll jump back to the place your cursor started at.
For instance, if you have your cursor on the line with "$help", and you double click on the $input_file entry in defs, the mark should show up on the line with $help, and Ctrl-, should return you to that line.
You can change it to not add marks to the gutter for pushed bookmarks, by unchecking the "Show pushed bookmarks" setting under Tools -> Options -> Editing -> Bookmarks. That won't clear any existing marks, but will make it so future push-tag's won't add any more marks.
