I'm sorry but I'm at a loss here. Your save file is missing starting area resources but in RSO state it says they were spawned. If you go exploring other resources are generated normally (at least for me). When I create a new game with same seed I get normal starting area resources.
Can you do the following:
1. Extract RSO and edit config.lua - change debug_enabled line to true
2. Start new game
3. Run following command in console after few seconds: /c remote.call("RSO", "saveLog")
4. Post me content of script_output/logs folder in Factorio directory - there should be 2 log files in there.