Thanks. I think maybe I see the problem. The command uses SendWin for one of the windows. SendWin changes the foreground window. Could you try rewriting the command with TargetWin like this:

Code:
//-----------------------------------------------------------
// SUBROUTINE TO Position Windows.
//-----------------------------------------------------------
<Command ResizeAndPosition>
<SendPC Local>
	<TargetWin %1%>
		<SetWinRect 384 0 1536 1200>
	<TargetWin  %2%>
		<SetWinRect 0 0 384 300>
	<TargetWin  %3%>
		<SetWinRect 0 300 384 300>
	<TargetWin  %4%>
		<SetWinRect 0 600 384 300>
	<TargetWin  %5%>
		<SetWinRect 0 900 384 300>