Thanks for the quick reply Xrobau - I read on another site that Engin don't allow CID from other providers to be set at the FreePBX end. I was able to ring Engin and get them to set our primary number as the CID as a mask for all calls from the Engin SIP trunk. It will take 24 hours to see if this works.
Its not perfect but better than turning CID off completely.