I have batch file that sets up the desktop environment for me when I am writing code. The file is named: SetEnv.cmd and it opens 3 other windows:
Try launching your programs from VBS (Windows Script Host) script via the batch file. If your VBS looks like this:
'FILENAME: SetEnv.vbs
Set Shell = WScript.CreateObject("WScript.Shell")
Shell.Run "Explorer /n,c:\develop\jboss-4.2.3.GA\server\default\deploy", 4, False
Shell.Run "Explorer /n,c:\develop\Project\Mapping\deploy", 4, False
The 4 means to launch the window in its most recent size/position. False means it won't wait to return before executing the next line of your script. Unfortunately, this doesn't give you full control of your exact window size/positioning, but it should remember last size/positioning.
More info here: http://www.devguru.com/Technologies/wsh/quickref/wshshell_Run.html
So your new SetEnv.cmd could be:
@echo off
REM note there's a difference between cscript and wscript
REM wscript is usually the default launcher
cscript SetEnv.vbs
cd C:\develop\jboss-4.2.3.GA\bin
run