The first thing I would check is to make sure that your JavaScript files are tagged. Do they belong to a project in your workspace? You can retag only the active project by going to Project > Retag Project, or you could retag everything with Tools > Retag Workspace.
After you have done this, open up the tag files dialog at Tools > Tag Files, select the appropriate project tag file in the left pane (they will be listed under the 'Workspace Tag Files' category), and look for your JavaScript files in the list in right pane. If they are not there then they are not being tagged, and this is a different problem.
If they are listed (and you confirm that you still aren't seeing tagging information in the Outline view), the next thing I would do is make sure that you haven't turned on any special filters. Right-click in the Outline view and do Quick filters > Show all tags. Any luck?
If it's still not working, then is it possible for you to post one of the offending files here so that I could take a look myself?
- Ryan