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If you're talking about Crimson, I've noticed that problem quite frequently. It may be whenever the monitors sleep, or whenever a remote connection has been made, or both.
The solution is to kill the cnext.exe process, then restart it with the "atlogon" parameter, while in the executable's directory. So either use the command line and navigate to that directory (C:\Program Files\AMD\CNext\CNext unless you change the install directory) and type "cnext atlogon", or create a shortcut that does the same.
After that restart, the settings will work again.