Installation problems
If the Movie Timeline toolbar is not visible in the list of available toolbars, check the STK Message Viewer for any "plugin" error messages that may have appeared on startup. Make sure you are running at least STK version 9, and the plugin has been installed. If you are certain the plugin is correctly installed, launch STK, click on Edit->Preferences, and select UI Plugins.
On the bottom half of the above screenshot, there is a "Reset Toolbars" button. Try clicking this button (with the Movie Timeline plugin selected in the upper part) to restore the default toolbar for the plugin.
Connection problems
The image in the previous section also identifies a small button that provides access to some internal settings within the Movie Timeline plugin. If you click it, you see a window similar to the one below.
The "Verbose Viewer Message Log" can be set to "true" to see a detailed log of communications between the plugin and STK in the Message Viewer window.
Turning on this setting will hurt the overall performance of the Movie Timeline plugin, and of STK itself. The setting may remain switched on in future STK sessions, even if you do not "set as default," until you manually turn it off again.
The verbose log is a good way to look for errors, malformed commands, or other communications problems between STK and the plugin. For example, if your timeline uses a Stored View that has been deleted or renamed in STK, errors will crop up here.
Remember to turn it off once the issue has been resolved, to improve performance.
Preventing the Timeline from Opening on Scenario Load
You can disable the Movie Timeline from appearing automatically when loading a scenario. To do that, click 
next to the active movie track, close the timeline, and re-save the scenario.