Your CHs don't lose their mapping, they're just in their default purely un-programmed DirectX-mode when you start up your computer. You simply have to switch them into the programmed AKA mapped mode, either manually via the CM or the CMCC, or automatically via the CMStart utility:
"CMStart is a small utility that you can use to reactivate your Control Manager map file at Windows restart. Normally, the Control Manager starts in "Direct" mode and to get the map activated you need to run the Control Manager and click the "Enable Map" button. CMStart will do this automatically without the need to run the Control Manager each time.
To use CMStart, you need to create a shortcut to CMStart.exe in your "StartUp" folder. The CMStart.exe file is located in the folder where the Control Manager was installed. The method for adding a program to the StartUp folder varies between Windows versions. See Windows Help for more information on how to do this." (Taken from the CM's online-help.)