I also have had this same problem in Recording Control, my balance and Volume level on Stereo Mixer never stayed at center after rebooting. I got it to keep my settings as default by doing the following:
1. Make a major adjustment to the items I wanted changed (balance to extreme left, volume all the way up), then close the Recording Control.
2. Reboot.
3. Make the desired adjustment to the items I wanted to change (balance to center, volume to about 25%), then close Recording Control.
4. Reboot and check.
So far, it's worked for me! I guess the mixers 'ignore' minor changes... Good luck!