A bit of oil stays in the engine when you drain it on the sidestand. Once it's finished draining...I tilt it over to the right and then back on the sidestand and get another 1/2 quart.
Try it next time.
Also - it's pretty tough to get an accurate read on the dipstick since you have to hold it level...plus, they are notorious for being innaccurate.
Next time you change your oil and shake it out....add 3.9 quarts. Ride it then park it where you usually do. Next day before you do anything....take the dipstick out and file a mark where it is cold on the sidestand. That way, you can check it like that instead of doing the acrobatics the manual calls for.
'04 1300 C, black, RIP
'04 1300 C, orange, for now
shut up and ride