I'm having a similar issue. Sometimes I have to save a preset multiple times before the lights will work properly. I have certain presets that I need particular lights to go black while others are in use. It seams like the easiest way to do it for me is this. Let all the lights run while you choose your color and motion preset values. After you are happy with the colors, motion, and selected sound, BPM, or timer you may then go change the dimmer slider for the lights I want off manually. Then I am able to save my preset.
Even after saving my preset and starting the next one, it seams like once I save the second preset it will get confused with the first preset and I have to repeat the steps again for the second preset.
Sometimes it takes me 2 or 3 tries to get a preset how I like it. All my presets will be saved I'm happy, then out of no where, the buttons for sound, BPM, and timer have decided to change themselves to the timer making me feel like my lights lost connection. So there I am again rewriting my presets.