your start bat is should kinda look like this, not sure how you are starting minilogin.exe. But try this and see if it helps.
Code:
@echo off
start MiniLogin.exe
sleep 5
start world.exe
echo Waiting for World to finish before starting Zone...
sleep 20
start eqlaunch.exe zone
sleep 40
and try to put this # in front of these lines and see
Code:
#loginserver2=newlogin1.eqemulator.net
#loginport2=5999