Behavior:

The OperationTimeoutException depends on the amount of records.

Entities:

[Serializable]
[HierarchyRoot]
public class TestA : Entity
{
  public TestA( Session session ) : base( session ) { }

  [Field, Key]
  public int Id { get; private set; }

  [Field]
  public int Val { get; set; }
}

[Serializable]
[HierarchyRoot]
public class TestB : Entity
{
  public TestB( Session session ) : base( session ) { }

  [Field, Key]
  public int Id { get; private set; }

  [Field]
  public int Val { get; set; }
}

Init:

using( var session = domain.OpenSession( new SessionConfiguration( SessionOptions.ServerProfile ) ) )
{
  using( var transaction = session.OpenTransaction() )
  {
    for( int I=0; I < 0x01FF; I++ )
      new Model.TestA( session );
    // To much records???
    for( int I=0; I < 0x01FFF; I++ )
      new Model.TestB( session );
    transaction.Complete();
  }
 }

Exception:

using( var sessionA = domain.OpenSession( new SessionConfiguration( SessionOptions.ServerProfile ) ) )
{
  using( sessionA.OpenTransaction() )
  {
    sessionA.Query.All<model.testa>().Count();
    sessionA.Query.All<model.testb>().Count();
    using( var sessionB = App.Domain.OpenSession( new SessionConfiguration( SessionOptions.ServerProfile ) ) )
    {
      using( sessionB.OpenTransaction() )
      {
        sessionB.Query.All<model.testa>().Count();
        // Exception
        sessionB.Query.All<model.testb>().Count();
      }
    }
  }
}

Exception:

using( var sessionA = domain.OpenSession( new SessionConfiguration( SessionOptions.ClientProfile ) ) )
{
  sessionA.Query.All<model.testa>().Count();
  sessionA.Query.All<model.testb>().Count();
  using( var sessionB = App.Domain.OpenSession( new SessionConfiguration( SessionOptions.ClientProfile ) ) )
  {
    sessionB.Query.All<model.testa>().Count();
    // Exception
    sessionB.Query.All<model.testb>().Count();
  }
}

No Exception!!!

using( var sessionA = domain.OpenSession( new SessionConfiguration( SessionOptions.ServerProfile | SessionOptions.AutoTransactionOpenMode ) ) )
{
  sessionA.Query.All<model.testa>().Count();
  sessionA.Query.All<model.testb>().Count();
  using( var sessionB = App.Domain.OpenSession( new SessionConfiguration( SessionOptions.ServerProfile | SessionOptions.AutoTransactionOpenMode ) ) )
  {
    sessionB.Query.All<model.testa>().Count();
    sessionB.Query.All<model.testb>().Count();
  }
}

Exception Message:

  
Xtensive.Orm.OperationTimeoutException was unhandled by user code
  Message=SQL error occured.
SQL error details 'Type: OperationTimeout;'
Query 'SELECT CAST(COUNT([a].[Id])  AS bigint) AS [c01umn] FROM [TestB] [a];'
Original message 'SQL Server Compact timed out waiting for a lock. The default lock time is 2000ms for devices and 5000ms for desktops. The default lock timeout can be increased in the connection string using the ssce: default lock timeout property. [ Session id = 5,Thread id = 3436,Process id = 2952,Table name = __SysObjects,Conflict type = s lock (x blocks),Resource = RID: 1658:13 ]'
  Source=Xtensive.Orm
  StackTrace:
       at Xtensive.Orm.Providers.Sql.StorageDriver.ExecuteCommand[TResult](Session session, DbCommand command, Func`2 action)
       at Xtensive.Orm.Providers.Sql.StorageDriver.ExecuteReader(Session session, DbCommand command)
       at Xtensive.Orm.Providers.Sql.Command.ExecuteReader()
       at Xtensive.Orm.Providers.Sql.SimpleCommandProcessor.ExecuteTasksWithReader(QueryRequest lastRequest)
       at Xtensive.Orm.Providers.Sql.SessionHandler.<xtensive.orm.providers.sql.iqueryexecutor.executetuplereader>d__0.MoveNext()
       at Xtensive.Orm.Providers.Sql.SqlProvider.<onenumerate>d__9.MoveNext()
       at Xtensive.Orm.Rse.Providers.ExecutableProvider.<getenumerator>d__0.MoveNext()
       at Xtensive.Core.EnumerableExtensions.<batch>d__20`1.MoveNext()
       at Xtensive.Core.EnumerableExtensions.<applybeforeandafter>d__28`1.MoveNext()
       at Xtensive.Orm.Rse.RecordSet.<getbatchedenumerator>d__c.MoveNext()
       at System.Linq.Enumerable.WhereSelectEnumerableIterator`2.MoveNext()
       at Xtensive.Core.EnumerableExtensions.<batch>d__20`1.MoveNext()
       at Xtensive.Core.EnumerableExtensions.<applybeforeandafter>d__28`1.MoveNext()
       at System.Linq.Enumerable.<selectmanyiterator>d__14`2.MoveNext()
       at System.Linq.Enumerable.First[TSource](IEnumerable`1 source)
       at lambda_method(Closure , Object[] , IEnumerable`1 , Session , Dictionary`2 , ParameterContext )
       at Xtensive.Core.DelegateBindExtensions.<>c__DisplayClassd`6.<bind>b__c(T2 arg2, T3 arg3, T4 arg4, T5 arg5)
       at Xtensive.Orm.Linq.TranslatedQuery`1.Execute(Session session, ParameterContext parameterContext)
       at Xtensive.Orm.Linq.QueryProvider.Execute[TResult](Expression expression)
       at System.Linq.Queryable.Count[TSource](IQueryable`1 source)
  InnerException: System.Data.SqlServerCe.SqlCeLockTimeoutException
       Message=SQL Server Compact timed out waiting for a lock. The default lock time is 2000ms for devices and 5000ms for desktops. The default lock timeout can be increased in the connection string using the ssce: default lock timeout property. [ Session id = 5,Thread id = 3436,Process id = 2952,Table name = __SysObjects,Conflict type = s lock (x blocks),Resource = RID: 1658:13 ]
       Source=SQL Server Compact ADO.NET Data Provider
       HResult=-2147467259
       NativeError=25090
       StackTrace:
            at System.Data.SqlServerCe.SqlCeCommand.CompileQueryPlan()
            at System.Data.SqlServerCe.SqlCeCommand.ExecuteCommand(CommandBehavior behavior, String method, ResultSetOptions options)
            at System.Data.SqlServerCe.SqlCeCommand.ExecuteReader(CommandBehavior behavior)
            at System.Data.SqlServerCe.SqlCeCommand.ExecuteDbDataReader(CommandBehavior behavior)
            at System.Data.Common.DbCommand.ExecuteReader()
            at Xtensive.Orm.Providers.Sql.StorageDriver.<executereader>b__4(DbCommand c)
            at Xtensive.Orm.Providers.Sql.StorageDriver.ExecuteCommand[TResult](Session session, DbCommand command, Func`2 action)