In some cases the Control Bar may seem to disappear on smaller screens. This is often because it’s anchored to the Stage (The full work area in the Toolbox), positioning it at a static distance from the centre of the stage. Often this happens if the eMag was created directly in the Toolbox - skipping the Wizard step. In the Wizard, the Control bar is anchored to the Publication by default to make it position itself accurately on all screen sizes.
To correct this, anchor your control bar to the catalog using the anchoring tool. For a quick introduction to the anchoring tool, take a look at this video: http://www.youtube.com/watch?v=QcWLBIaSg-Q on the eMagStudio YouTube channel.