When you look at the registy of a x64 System you will notice that there are some keys in there called Wow6432Node. These keys are there for 32-bit applications.
Basically if you have a 32-bit application that is reading from the registry in the key “HKEY_LOCAL_MACHINE\SOFTWARE\<company>\<product>”
it is actually reading from “HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\<company>\<product>”.
You can turn of this behaviour in your code by using dllimport and so on. pretty complicated. Read all about it here.
A simple work arround ofcourse is to store you registry settings in the Wow6432Node.