Wow6432 node will be found on a 64 bit windows. This is used to provide a 32 bit environment for your application in 64 bit system. I assume your application is 32 bit. Hence, when it tries to read the Registry values, it will be redirected to the Wow6432 node.
May be, you can add a custom registry key under HKCU to decide whether to run the app or not after starting up from Wow6432 node as mentioned above.
That is add your startup entry here:
HKLM\SOFTWARE\Wow6432Node\Microsoft\Windows\CurrentVersion\Run
An then, add a custom entry in HKCU for deciding whether to continue running the app or to close it.
I mean, you can add a separate logic in your application for that.