I also suspect that there is something Scans interfere with your scanner.
Since the error follows the scan direction, the problem is probably the scan unit (not the glass).
Scanners using CIS (Contact Image Sensor) can be located on the "light guide" that is in close contact with the scan surface. For scanners with CCDs, the problem may be with a number of mirrors or the lens in front of the sensor.
If you ever loosened the glass from the scanner body, you may have reset it to the sensor with the wrong side. The glass could have coatings on one side which are required to prevent reflections from interfering with the scan. The same applies to all other components between sensor and target.