I am curious what I need to do to get the header bar to not display over my figure in matlab. It partially covers a button. I can provide more information if requested.

I call using VB from powerpoint:
Call RunFile("WindowAPI(new_control_pan,'Clip',true)", "C:\Users\mhaartman\Documents\PANE_golden2\PANE_golden\code")
and I still see the same thing.
Your question needs more clarification.. In the meantime, you can hide the menu bar and the toolbar as such:
the resulting figure looks like:
if you are on MS Windows, we can go even further and remove the window borders (make it look like a splash screen). This is done by calling native Win32 API from a C MEX-function (I am using the WindowAPI function by Jan Simon on the File Exchange)