That's pretty funky. What I would advise is to open up another instance of VSB
with default Aero loaded and do a quick check in the properties section between each part of the Start menu.
I have a feeling you accidentally copy & pasted a RECT property with your own custom values into the Logoff/LogoffButtons section of Aero/Basic Start Panel which is pushing that area down and clipping it as it is partially out of bounds.
Edit: I just went ahead and checked, and my guesses were right -- at least for me, I hope they help you out as well. If you manually added the RECT property into the Aero Logoff section (doesn't matter if it's Top or Bottom, it's inherited from either/or), you can move it around.
I'm going to play with it some, maybe I can align things better. You can also 'delete' the area by entering 0, although I have no clue why you'd want to do that (I'm still confused with themes stripping the right panel off and hiding the searchbar, but whatever). Thanks for getting me to find this