Well, having the folders in EnergyPlus read-only certainly
won't help with creating batch files there. It's not a
setting from EnergyPlus install. EnergyPlus depends on being able
to write files in the main root folder.
Did you read the article Tianzhen suggested?
Take a look at the recent issue of the Building Simulation User News at
http://gundog.lbl.gov/dirun/Newsletter2009_1.pdf. Your question
should be answered at the "Ask an EnergyPlus Expert"
section.