This was the result of a combination of factors.
First, we stop monetdb on Instaview project close and start monetdb when a new Instaview project is created or an existing one is opened up.
Second, we recently started Pooling our monetdb connections in agile-bi for analyzer/mondrian. However, the configuration of the pool was such that it didn't do a validationCheck of the connections before handing them out. So, as one could imagine, when you walk through a project and get into analyzer the connection pool is created for the first time and all connections are good. as soon as you close that project, the monetdb service is stopped and that forces all connections in the pool to no longer function. Subsequent requests for connections from the connection pool would just blindly hand these invalid connection back out.
The fix was to add a validationQuery to the PoolableConnectionFactory used as well as set the testOnBorrow flag of the GenericObjectPool. This in effect makes the connection pool "test" the connection it has before handing it out with the validationQuery (in this case it is simple "SELECT 1"). if it fails, it creates a new connection.