Well, placing them on the Tomcat > JDK preference page in the Optional VM Arguments box, one per line like:
-Dprop1=value
-Dprop2=value2
Should do the trick. I was unable to reproduce any problem with this behavior. However, I’m testing on the candidate GA release build which will be available on the website tomorrow. In any event, I highly recommend upgrading the the new release when it becomes available.
–Scott
MyEclipse Support