I read the whole paragraph and could not find a question, so I will try a few suggestions. When you scan, select the option to open the scanner interface. It will give you more control on what you scan.
From the flatbed When the scanner interface appears choose to Preview the scanned area. On the preview image click neat its border and you will see a dotted/ interrupted frame. Play with the borders of the frame to select the area. Intelligent software like Adobe Acrobat rotate the image to right it.
From the ADF Check the alignment of the paper on the document feeder. Test the first page and see if it is correct. If it is, and all the subsequent pages have the same margins use the ADF If not, maybe you should use the flatbed.
Answers & Comments
I read the whole paragraph and could not find a question, so I will try a few suggestions.
When you scan, select the option to open the scanner interface. It will give you more control on what you scan.
From the flatbed
When the scanner interface appears choose to Preview the scanned area. On the preview image click neat its border and you will see a dotted/ interrupted frame. Play with the borders of the frame to select the area. Intelligent software like Adobe Acrobat rotate the image to right it.
From the ADF
Check the alignment of the paper on the document feeder. Test the first page and see if it is correct. If it is, and all the subsequent pages have the same margins use the ADF If not, maybe you should use the flatbed.
OOPS neat should be NEAR