[Win32Exception (0x80004005): The wait operation timed out

I am receiving the following error on one of our C# MVC applications. The application is sat on top of AWS. The application talks to SQL server on another Amazon AWS instance.

The problem we have is that the issue does not occur all the time. It happens every night and can only be resolved by resetting the firewall rules on AWS. It has also happened occasionally during the day.

What is also strange is that we have another web application on the same instance connecting to the same remove SQL database and that application never gets this error.

The application with the error is running entity framework, so wondered if that plays any part in this.

[Win32Exception (0x80004005): The wait operation timed out]

[SqlException (0x80131904): A network-related or instance-specific error 
occurred while establishing a connection to SQL Server. The server was not 
found or was not accessible. Verify that the instance name is correct and 
that SQL Server is configured to allow remote connections. (provider: TCP 
Provider, error: 0 - The wait operation timed out.)]