Is your server Mac or Win? Mac has driver connection limits. Depending on how your script is written and how quickly the previously used connections are released you may be seeing that problem. If this is the case you might be able to reorganize how this process is done or contact Actual Technologies for a special licensing package to accommodate your use.
Thanks for your reply BigTom, the solution is hosted in Windows Server 2012, so it's not a Actual Tech driver issue. I actually think I've resolved this now by using the Set Field script step over the ESS instances rather than the Execute SQL 'Insert' script step, and this seems to have resolved the issue - I guess it was something to do with creating and releasing the connection, perhaps at the remote end.
Thanks for your response.