Yep. That's what's happening here. We import EDI orders via Edisoft's Merchant software. That software doesn't interface natively with Adagio, but uses the ACCPAC interface instead. As a result, EDI orders get 'entered' into ACCPAC OE. When we subsequently launch Adagio OE, it displays the message Acrylon mentions.
In our case, we understand why this is happening - so it's not a problem for us. We have been told Edisoft is working on an Adagio version of its software, which should make those messages go away.