pilotinsky, Are you talking about this happening in flight? If so it is because there is not enough electrical load for the alternators to share, This happened alot to me on long cross counrty flights, I would get one alternator that would pick up the entire load and when I would shut that alternator down the other alternator would take up the load. Try turning on your nav, landing lights and and any other light that would place additional load on the alternators to see if they both would then start sharing the load.

As far as engine restarts in flight I always leave the avionics master on in flight and during restart it would not shut down. However you may be leaving the starter on for too long which would cause a large drain on your remaining alternator. I would try engaging the starter for up to 5 seconds, if the engine does not start give the alternator a chance to stabilize around 20amps and then try again. This will help to curtail the load being placed on the alternator.