The problem is occuring at least since mustang b45 and up to mustang b53.
When saving some changes using Control Panel on Windows platform, they are saved in "deployment.properties" file as:
deployment.javapi.jre.1.6.0.args=
deployment.javapi.jre.1.6.0.osname=Windows
deployment.javapi.jre.1.6.0.osarch=x86
deployment.javapi.jre.1.6.0.path=C\:\\Program Files\\Java\\jre1.6.0

while on Unix platforms they are saved as:
deployment.javapi.jre.1.6.0-ea.args=
deployment.javapi.jre.1.6.0-ea.osname=Linux
deployment.javapi.jre.1.6.0-ea.osarch=i386
deployment.javapi.jre.1.6.0-ea.path=/set/stt/jdk_promotions/JDK6.0/b52/binaries/linux-i586/jdk1.6.0/jre

Is it ok, that "-ea" in the name of the properties is present in Unix and is not present in Windows "deployment.properties"?