I too have this issue. If you stop scrolling for 5 seconds because your reading, then go to start scrolling again, there is a freeze or delay of about 1 second. its noticeable, and very annoying. There are no viruses, and its not a plugin. (I don't use chrome extensions or plugins.) Safari doesn't have the issue, and its machine specific. The identical Chrome on an older iMac, identical OS, doesn't have the issue.
My guess is that chrome has "frozen" the page, to save on CPU cycles, and has to release that and start live rendering it again when it sees you start scrolling. Or maybe its a delay of swapping between graphics mode on the hardware...?
Some interesting extra notes...if a text editor panel is open, such as the one you comment on here, the issue does not exist. If an active video such as on youtube is playing in the window, then there is no lag scrolling either.
If you are scrolling up, there is never a delay, its only scrolling down that has the delay.
You see the mouse pointer change for the items that would be scrolling under it before you see the page even move. So this indicates its some lower level thing that is going on, and most likely graphics related.
Best Answer
Go to chrome://flags/#views-browser-windows and select Disabled on the dropdown for the "Use Views browser windows instead of Cocoa" flag. Relaunch Chrome.
This should bring the old behavior back, with one caveat: it will bring the old design back too.
This flag has been removed in chrome 71 so there is no way to change the behavior from 71 onwards