Ok,
1. You only need to flash the bios once. If your 1.6 xbox works with the current bios, you're set!
2. If Evox is loading up you dont need to flash anything. Changed settings in evox save automatically. Evox runs off the harddrive and the settings/everything is saved there. A bios just boots the box up (starts the hdd, dvd drive, etc, checks if games are originals or not, thats why modchips let you play backups - its not really the modchip its the bios. Modchips only let you change the bios

). If evox boots up, thats (essentially) all your bios should be doing. Any problems other than that is something other than your bios.
That hopefully answers all your questions.
Oh, and try san andreas without changing any settings. What works for me is: put san andreas in your dvd drive. Turn the xbox off, leaving the game in the drive. Then turn it on again and it should boot (works for me, I have a 1.0 xbox, xecuter2 5035 bios and duox2 modchip). Try that first before changing settings.