The .properties file is added to the JAR when you package your bot, but it shouldn't be needed in order to see a development version of your bot. I'm not sure, but I think you'll need to add the top level directory in Robocode - e.g., if your bot is zjk.MyRobot, under ...\build\classes\zjk\MyRobot.java, you'd need to point Robocode to ...\build\classes.
I have my things setup the other way, with Eclipse compiling the .class files into robocode/robots/, but that's kind of a stupid setup that I've just never bothered to change.
Not that stupid. Many times I saw a development version working, only to generate a non-working JAR. Wrong .properties file, security violations, wrong file names...
And the opposite problem (non-working development versions) arises when you use the engine API directly instead of the GUI . i.e. genetic tuning with full battles.
I also develop and test using JARs instead of raw .class files.