The only problem I consistently have with my custom settings is the fact that it always reverts the aperture and shutter speed back to what was set when the custom setting was registered. So, if your custom setting was registered with an aperture value of f/1.4, but you happen to be shooting mostly at f/8, then you can run into screw-ups if you switch off your camera for a few moments. You can turn your camera back on thinking you're still set on f/8, but the camera has reverted back to f/1.4. Same applies with ISO settings. So, if I'm on a photowalk, it's often more convenient for me to just use full manual mode "M", since the other modes remember the previously used settings rather than reverting back to a registered custom setting.
That said, I still use C1-3 most of the time in my shooting and my biggest complaint about the custom modes is that there's only three of them...I could use a couple more.
There's an option to enable "Auto update set" when on you're on custom mode. If enabled, it will automatically register any changes you've done while shooting on a specific custom set.