1. Based on the past, I never trust 'new' batteries; always check voltage.........cell batteries, that is.I have bought W220, 2001, S500 last week. It have 165k Kilometers on the clock and works perfectly fine beside only one issue. It does not lock or unlock from the key. I have to align the key to the door handle to get it lock/unlock. I got the car scanned but there were no errors displayed. I replaced the FOB batteries as well but it didn't work.!! KEY is perfectly fine as well, Light blinks on every button click. Looking for help.!!
2. Windows, sunroof, head-restraints, etc must be synchronized every time main battery is disconnected. I am not sure about your Model/year as to whether door locks fall in this category. If all else fails, I've found MB Service Managers pretty friendly in giving advice if approached with further-business-in-mind
3. Check this out: 2001 S430 doors won't lock with remote - MBWorld.org Forums