Any errors displayed in the bot console when it crashes?
From what others have said regarding AoC timeouts, you will need to wait at least 5 minutes for the Bot's connection to the gameserver to time out. Although this could be client side dependant and not server side dependant for all i know.
Bottom line is that since patch 1.05, Funcom have made life very difficult for anyone running a bot and there is very little we can do. And from the sound of what you describe here, it could indicate that you are connecting using the client before the bot's connection has died, which will lead to both the bot and the client being "locked out" until you restart both.