Right now base swap is done before server.cfg and map.cfg are executed, which means it's unusable. Make it execute after server.cfg and map.cfg.
The way base swap is currently implemented leaves it with a lot of issues unless you use it very very carefully. Unfortunately there is no easy fix so try to avoid enabling this option.
You do the base swap command then restart the map.. But it is limited to certain maps. I think they are listed in a script file.