The eConnect nodes for SOP transactions behave differently than any other nodes.
Normally, when the Update If Exists option is checked, the eConnect nodes will insert new records and update existing records. With the SOP transaction nodes, when the Update If Exists option is checked, the nodes will only do updates to existing records.
To resolve this, use one SOP transaction map to insert new records and leave the Update If Exists option unchecked and use another map that only does updates to existing SOP transactions where the Update If Exists option is checked.
Another resolution to this issue is to set the value of the Update If Exists parameter to true (1) if the SOP Line exists or the SOP Header exists and false (0) if the SOP Line does not exist or SOP Header does not exist using a Calculated Column.