As mentioned above, begin your project with a template that has everything arranged as you like.
To build such a template, start with a blank ‘new project’, set things up for your favorite work-flow scenarios and save them as Workspaces. Save the empty project once you’ve set things up.
You can create entire 'Workspaces" which will remember the size, locations, and topping order of all your open windows. Workspaces can be assigned to key-combos.
Is it being ‘closed’ or simply falling back behind other windows?
If it is actually being ‘closed’, are you changing to Workspaces that might not have had the transport controls open when you saved the setup?
For me (Windows 7, CuBase 220.127.116.118 Pro 64bit), Transport usually stays the top window once I open it, and does NOT go away unless I close it (usually by toggling the F2 key) with only a couple of exceptions:
 Selecting a different “Workspace” that does not include the Transport Controls window.
 large plugin windows (I.E. Halion 5) can top the transport bar.
[*] Some of the settings windows or dialogues can top all other windows.
CuBase 8 can do some things that earlier versions did not allow, that can sometimes cover or hide other windows or dialogues. I.E. With CuBase 8, you can drag windows to different screens/monitors.
CuBase 8 Pro spread across three monitors.
( Two side by side at 1024 X 768 and one centered underneath @ 1280 X 1024 )
Due to the new abilities intended to better support multiple screens, some windows have new options on their behavior. I.E. If you open a VST plugin, you might find in its options menu (usually somewhere in the upper right hand corner of the plugin window) that it can be set to ‘always stay on top’. Always top seems to be the default for plugins. When that is enabled, it can cover your transport controls.
Here you can see how the Eighty Eight Ensemble plugin is topping ALL windows that I have open in this shot.
I could change that behavior by toggling “Always On Top” so the check-mark disappears.
If you loose a window due it having been ‘topped’, you can usually bring it back to the top layer with the “Window” menu.
An exception might be if a large Plugin window is active and set to ‘Always Top’. In that case, you’ll need either close the Plugin window, re-position it, or toggle it so it’s not ‘always on top’ to see whatever is ‘under it’.