Is it possible I have more than one registry on a single Windows 7 ins

Is it possible I have more than one registry on a single Windows 7 installation? Could that be the result of an in-place upgrade?
I ask because while trying to sort out a Java install error it does not appear to be in the correct registry folder.
I'll explain: When I use regedit and navigate to HKEY_LOCAL_MACHINE/SOFTWARE/MICROSOFT/WINDOWS/CurrentVersion/Uninstall there is no entry for Java.
However, if I use Revo Uninstaller Pro, right click on java and select Open registry Key from the context menu it takes me right to it. So I look at where I am and it's the exact same place. HKEY_LOCAL_MACHINE/SOFTWARE/MICROSOFT/WINDOWS/CurrentVersion/Uninstall
On closer inspection none of the keys in that registry are the same as when I get there through regedit.
It looks like I'm headed for a Windows 7 clean install but is this even possible?

OK thanks. I forgot about the separate locations for x86 and x64 programs. I was was able to get Java installed properly now but I still get an error when I try to use the Nvidia GPU_Reader applet. It always worked before. Now I get the error "Java (TM) Platform SE binary has stopped working" when I try to run it from the Nvidia website. I do know how to get the Nvidia drivers without the reader but it would help me determine why when I download and install the latest drivers I end up with the same old ones. Clean drivers install doesn't help and the beta drivers install an earlier version then what is shown on the website. Any ideas?

Apparently the GPU Reader can only be installed from he Nvidia website. There is no actual download for it. Which is odd because on the site you sent me Nvidia tells how to uninstall it. It's not in my Manage add-ons folder. I tried running IE as an administrator from it's special icon in the start menu but that didn't help. I tried setting Java to it's lowest security level. No help. Is there a way to temporarily disable IE permissions requirements? More ideas?