bin/run.sh omits logic for parsing the long form of the configuration argument (--configure):

Relevant stanza:

arg_count=1
eval SWITCH=\${$arg_count}
while [ ! -z "$SWITCH" ]
do

if [ "$SWITCH" = "c" ]; then <----------no evaluation of --configure argument
eval JBOSSCONF=\$`expr $arg_count + 1`
CONF_SPECIFIED=true
break
fi

arg_count=`expr $arg_count + 1`
eval SWITCH=\${$arg_count}
done

Ian Springer has come up with a fixed version of run.sh, which is attached to this case.

This likely affects other versions as well, I have only tested on 4.3.0GA_CP03 and 4.2.0GA_CP05