You should call the command line executable, not the GUI application (which is what you're doing).
The correct executable is PK3CMD.exe and your parameter format looks a bit strange. Please see:

http://www.picbasic.co.uk/forum/showthread.php?t=12108
http://www.picbasic.co.uk/forum/showthread.php?t=14064

And, if you want to use the new IPE from MPLABX instead of the old PK3CMD.exe here's a thread on that subject:
http://www.picbasic.co.uk/forum/showthread.php?t=21149

/Henrik.