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Have you seen the values set to 1 and then noticed them revert back to 0? Or is the case that you presume MSP bundle register settings updated the values? You may want to check the key values before and after the MSP register setting deployment, and insure the values do get updated to 1.
You're correct in that warm-boot and cold-boot will not reset the registry.
However, if an unsuspected system initiated clean-boot is performed then that would be considered a corrupted enviroment; whereby a clean-boot is required to restore the file system and enviroment.
I think that I found the problem. Different devices had different version of that particular MSP setting but they were named identically. Thanks anyway for confirming that the cold boot does not reset the registry.