I have the same problem as rdefuria and csvanhoeven, on my i-SENSYS MF735cx.
Windows 10 (64-bit, April 2018 update), Canon MF Scan Utility v1.5.0.0, MF735cx driver v21.81, Canon MF735cx overall software package installer v5.4.0.0, MF735cx firmware is up to date (I don't recall what version, but this was confirmed two days ago by Canon support for other reasons).
Every time I scan from the platen glass from the scanner console by tapping Scan -> Computer, the computer to which the scan should be delivered pops up the message:
"Selected paper size is larger than physical scanning area.
Cropping will occur.
Continue?"
Looking at the http://{my MF735cx IP address}/ System Manager interface, the configuration for every scan type for paper size is A4. A4 is, obviously, not larger than the physical scanning area.
Canon, please help us fix this. It's a huge interruption to have to Every. Single. Time. ... we scan from the scanner to the computer, walk back to the computer to click "ok" to dismiss this erroneous prompt.
thank you,