(1024 works)

@echo off
IF EXIST "C:\atariii\Windower\scripts\init1024.txt" rename "C:\atariii\Windower\scripts\init.txt" init800.txt && rename "C:\atariii\Windower\scripts\init1024.txt" init.txt
start C:\atariii\Windower\launcher.exe -x 1024 -y 768

(800x600 works)

@echo off
IF EXIST "C:\atariii\Windower\scripts\init800.txt" rename "C:\atariii\Windower\scripts\init.txt" init1024.txt && rename "C:\atariii\Windower\scripts\init800.txt" init.txt
start C:\atariii\Windower\launcher.exe -x 800 -y 600
exit

(both the above swap around with no probs)

(640)

@echo off
IF EXIST "C:\atariii\Windower\scripts\init640.txt" rename "C:\atariii\Windower\scripts\init.txt" init1024.txt && rename "C:\atariii\Windower\scripts\init1024.txt" init.txt
start C:\atariii\Windower\launcher.exe -x 640 -y 480
exit