JSI Tip 10199. TaskBarCmd freeware sets the 'Auto-hide the taskbar' and 'Keep the taskbar on top of other windows' options from a command-line or batch.

Download the TaskBarCmd_1_0_exe.zip file and unzip it.

When you type TaskBarCmd /?, you receive:

TaskBarCmd 1.0; (c) Mihai Nita, Feb. 2006
Usage: TaskBarCmd \[option\] ...
  Long options:  -AutoHide, -NoAutoHide, -KeepOnTop, -NoKeepOnTop
  Short options: +AH, -AH, +Top, -Top
  Example: TaskBarCmd +AH -Top
    will enable autohide and will prevent the toolbar from staying on top

NOTE: The switches are case sensitive.