Sobre el tema de las alertas que no se ejecutaron, en el log se puede ver claramente que dan errores como este:
2016-05-28 23:27:00,004 [AppJobWinServiceScheduler_Worker-2] INFO Aseinfo.VH4.WindowsServices.ApplicationJobs.AlertaJob - Inicia la ejecución de alerta: 32DFB36E-8C98-404A-A0E8-F999C58F51DD
2016-05-28 23:27:00,004 [AppJobWinServiceScheduler_Worker-2] INFO Aseinfo.VH4.WindowsServices.ApplicationJobs.AlertaJob - Reconfigurando el contenedor de Unity de la alerta: 32DFB36E-8C98-404A-A0E8-F999C58F51DD
2016-05-28 23:27:00,004 [AppJobWinServiceScheduler_Worker-2] INFO Aseinfo.VH4.WindowsServices.ApplicationJobs.AlertaJob - Obteniendo los datos de la alerta: 32DFB36E-8C98-404A-A0E8-F999C58F51DD
2016-05-28 23:27:00,004 [AppJobWinServiceScheduler_Worker-2] INFO Aseinfo.VH4.WindowsServices.ApplicationJobs.AlertaJob - Obteniendo máximo número de caracteres que se pueden manejar en una columna de resultado de alerta: 32DFB36E-8C98-404A-A0E8-F999C58F51DD
2016-05-28 23:27:00,019 [AppJobWinServiceScheduler_Worker-2] ERROR Aseinfo.VH4.WindowsServices.ApplicationJobs.AlertaJob - Error al ejecutar la alerta
System.Data.Entity.Core.EntityException: The underlying provider failed on Open.
---> System.Data.SqlClient.SqlException: Login failed for user 'EvoDataUser'.
at System.Data.SqlClient.SqlInternalConnectionTds..ctor(DbConnectionPoolIdentity identity, SqlConnectionString connectionOptions, SqlCredential credential, Object providerInfo, String newPassword, SecureString newSecurePassword, Boolean redirectedUserInstance, SqlConnectionString userConnectionOptions, SessionData reconnectSessionData, DbConnectionPool pool, String accessToken, Boolean applyTransientFaultHandling)
at System.Data.SqlClient.SqlConnectionFactory.CreateConnection(DbConnectionOptions options, DbConnectionPoolKey poolKey, Object poolGroupProviderInfo, DbConnectionPool pool, DbConnection owningConnection, DbConnectionOptions userOptions)
at System.Data.ProviderBase.DbConnectionFactory.CreatePooledConnection(DbConnectionPool pool, DbConnection owningObject, DbConnectionOptions options, DbConnectionPoolKey poolKey, DbConnectionOptions userOptions)
at System.Data.ProviderBase.DbConnectionPool.CreateObject(DbConnection owningObject, DbConnectionOptions userOptions, DbConnectionInternal oldConnection)
at System.Data.ProviderBase.DbConnectionPool.UserCreateRequest(DbConnection owningObject, DbConnectionOptions userOptions, DbConnectionInternal oldConnection)
at System.Data.ProviderBase.DbConnectionPool.TryGetConnection(DbConnection owningObject, UInt32 waitForMultipleObjectsTimeout, Boolean allowCreate, Boolean onlyOneCheckConnection, DbConnectionOptions userOptions, DbConnectionInternal& connection)
at System.Data.ProviderBase.DbConnectionPool.TryGetConnection(DbConnection owningObject, TaskCompletionSource`1 retry, DbConnectionOptions userOptions, DbConnectionInternal& connection)
at System.Data.ProviderBase.DbConnectionFactory.TryGetConnection(DbConnection owningConnection, TaskCompletionSource`1 retry, DbConnectionOptions userOptions, DbConnectionInternal oldConnection, DbConnectionInternal& connection)
at System.Data.ProviderBase.DbConnectionInternal.TryOpenConnectionInternal(DbConnection outerConnection, DbConnectionFactory connectionFactory, TaskCompletionSource`1 retry, DbConnectionOptions userOptions)
at System.Data.SqlClient.SqlConnection.TryOpenInner(TaskCompletionSource`1 retry)
at System.Data.SqlClient.SqlConnection.TryOpen(TaskCompletionSource`1 retry)
at System.Data.SqlClient.SqlConnection.Open()
at System.Data.Entity.Infrastructure.Interception.InternalDispatcher`1.Dispatch[TTarget,TInterceptionContext](TTarget target, Action`2 operation, TInterceptionContext interceptionContext, Action`3 executing, Action`3 executed)
at System.Data.Entity.Infrastructure.Interception.DbConnectionDispatcher.Open(DbConnection connection, DbInterceptionContext interceptionContext)
at System.Data.Entity.SqlServer.DefaultSqlExecutionStrategy.<>c__DisplayClass1.<Execute>b__0()
at System.Data.Entity.SqlServer.DefaultSqlExecutionStrategy.Execute[TResult](Func`1 operation)
at System.Data.Entity.Core.EntityClient.EntityConnection.Open()
--- End of inner exception stack trace ---
at System.Data.Entity.Core.EntityClient.EntityConnection.Open()
at System.Data.Entity.Core.Objects.ObjectContext.EnsureConnection(Boolean shouldMonitorTransactions)
at System.Data.Entity.Core.Objects.ObjectContext.ExecuteInTransaction[T](Func`1 func, IDbExecutionStrategy executionStrategy, Boolean startLocalTransaction, Boolean releaseConnectionOnSuccess)
at System.Data.Entity.Core.Objects.ObjectQuery`1.<>c__DisplayClass7.<GetResults>b__5()
at System.Data.Entity.SqlServer.DefaultSqlExecutionStrategy.Execute[TResult](Func`1 operation)
at System.Data.Entity.Core.Objects.ObjectQuery`1.GetResults(Nullable`1 forMergeOption)
at System.Data.Entity.Core.Objects.ObjectQuery`1.<System.Collections.Generic.IEnumerable<T>.GetEnumerator>b__0()
at System.Data.Entity.Internal.LazyEnumerator`1.MoveNext()
at System.Linq.Enumerable.FirstOrDefault[TSource](IEnumerable`1 source)
at Aseinfo.Infrastructure.Base.Entity.EntityServiceBase`2.GetEntityById(IdT id, Expression`1[] includes) in c:\BuildAgent\work\89066541112bb801\Infrastructure\Base\Entity\EntityServiceBase.cs:line 309
at Aseinfo.VH4.WindowsServices.ApplicationJobs.AlertaJob.Execute(JobExecutionContext context) in c:\BuildAgent\work\89066541112bb801\VH4\WindowsServices\ApplicationJobsWindowsService\ApplicationJobs\AlertaJob.cs:line 121
Esto indica que la alerta no se ejecutó porque no tiene acceso a la base de datos. Esto apoya los comentarios que hiciste sobre cambios que hicieron en el servidor SQL.
Cada vez que se cambia la cadena de conexión en Evolution, o se cambian los permisos de los usuarios de conexión, se deben "Detener" las alertas y volverlas a "Iniciar", ya que como parte de los datos de las mismas se almacena la cadena de conexión que usa para ejecutarse.