Change the original orientation back to portrait.
In Workflow scan it is on the first screen
To change the defaults you need to be in CWIS:
Email is Properties > Services > Email > Setup > Defaults > Layout Adjustments > Edit
Default template is Properties > Services > Workflow Scanning > Default template > Layout Adjustments > Edit
And specific Templates are done in Scan where you select a template and scroll down to the Layout Adjustments section and change it there.
It also sounds more like the Original size is no longer set to Auto, so check for that as well since it is in the same place for each thing in CWIS. At the copier it would be under the Layout Adjustment tab in Workflow Scanning as well as Email
