broadley--Based on the Java JRE installation on my PC, it looks like it is normal to have Java files in both Windows/Program Files and System32. I do not know the function of those in System 32 (perhaps they are backup files to use in a Repair), but I suspect the ones that actually make Java function are those in Program Files.
Any reason why you refer to whatever is in the System32 folder as the "earlier" version? You have given the same version number to each.
The current version of Java JRE is 1.6.0_03 (which means version 6, update 3), though the java.exe file is version 6.0.30.5.
You do not mention that whatever is in the System32 folder is causing problems.
I suggest just leave them be.