Apart from not being paper-fed, your symptoms indicate calibration problems.
Calibrate under windows is fine - it is supposed to restore the scanner to factory conditions.
Overall, I think I need to be sitting in front of the scanner to help you properly.
Summary of scanner data:
found USB scanner (vendor=0x04a9 [Canon], product=0x2213 [CanoScan], chip=GL842) at libusb:002:011
device `genesys:libusb:002:003' is a Canon LiDE 35/40/50 flatbed scanner
GL842 is known to be troublesome - but sane lists the LiDE 30/40/50 as having "good" support.
I see lots of people with scanning issues with this scanner - but the prevailing fix is to buy a new scanner. If the scanner is in warranty, take it back. You could pay someone to look at it, but the lide 50 is a cheap thing so you are still better off with a new one. That's the main problem - the scanner is so cheap that people just replace it when something goes wron - as a result, nothing gets fixed or properly investigated.
I did, however, find a cute trick ... it involves selecting a slightly smaller area for the scan, zooming to that, then hitting scan.