Thats okay. Now start playback and see if your 000000030000003F was appied.
Settings are saving on the actual change, settings are loading on the actual need.
Actual change is your input, Actual need is the play button event.
Settings in stop mode are fake. Settings right after winamp loading is a bin trash. Always check and inspect your matrix while playing something.
All the settings are loading or saving at once. It does not matter what you change, the file will rewrite at its whole. The automate checkbox option will screw up the user matrix when enabled, as expected.