Multi-algo (12xxx) and multi-coin-single-algo (17xxx) auto switches wait until a block is found and then switch to another algo/coin. The only way to lose your shares is to stop mining before the pool finds a block, which unfortunately is what multi miners do on automatic mode.
Just a note that you are not guaranteed to lose your shares, it's just possible. When switching is kept to a minimum, so are the possible loses.
Each coin is its own separate pool and PPLNS is to prevent cheating not switching; 20xxx ports are the 'real' pools.
MultiPoolMiner should soon get TCP access to MiningPoolHub to eliminate this problem for good and will have live profits and found blocks.