Hi Eddie,
As you discovered CCS ships its own version of JRE, which it uses. It does not depend on system JRE nor other CCS versions JRE.
One possibility may have been with write permissions. When RTSC products are discovered, they get registered with CCS. This process needs write permissions to installation directory to be able to make that "registration". CCSv4.x is based on a relatively old version of eclipse when user account permissions on windows was not use much. CCS v5.x is a little bit better as it is using newer version of Eclipse.
Martin