Custom user registry configuration change after deployment

In our standalone(non-clustered) environment, whenever we deploy any ifix or any new version of RAM the "use a custom user registry" check-box in the Configuration page of RAM gets unchecked by itself. This is in spite of the fact that before server upgrade, that check-box use to be checked. This is always the case with standalone environment and never with clustered environment.
Can you please let us know if this issue use to happens sometimes in standalone environments and what may be the cause of it?

Thanks.....Payal