Please consider making sync with EndnoteWeb and “find reference updates” silent process, that is without the pop-up box. Since these can take a while (especially if you have a lot of PDFs), it is terribly inconvenient to have the process take over the entire program, making note-taking, reference updates, and working CWYW impossible to access. Look at your competitors (e.g. Mendeley) for example, where these sort of things are happening behind the scenes with only a little notice in the status bar telling you that they are happening.
If I were you, I would add sync and “find reference updates” status to the left-hand column under “find full text,” which I would rename something like “Online Activities.”