I have to use ClearCase at work and the basic workflow requires me to do something like:
cleartool setview
view
If your workflow was to start emacs and then set into a view from there, things will be strange indeed.
The only thing that setview does differently from startview is that it starts that chrooted shell. Only that shell, and its descendants, will see source code in /vobs/vobtag/... If you work in multiple "setview" shells (for multiple versions of your app to maintain, multiple phases, etc.), you would have multiple otherwise identical shells accessing different versions of the same files via apparently-identical paths.
One thing to be aware of when working with ClearCase is that directories are versioned too. As a result, files added in one view may not appear in the other view if:
Unless your build process requires VOB contents to be visible at /vobs/vobtag, I'd concur with @VonC about not using setview.
I can't really add anything to VonC's other comments.