AWE should not be enabled on 64bit systems.

Does the server have 16GB of memory total? If there is only 1.2GB available you are choking the OS, that can seriously impact things that the ETL process can require.

Do you have the "Lock Pages in Memory" setting on for the service account that you are using?

You mention the virtual memory, you should not be paging at all, so this should be irrelevant, if you are seeing paging it is because you either have only 1.2GB for the OS, or it's paging out SQL processes in order to run OS processes.

Make a start with those things and if you get no improvements then you'll need to provide schemas, scripts and data examples.