Unable to reproduce the issue on MAC 10.11.6, Windows 10 and Ubuntu 14.04  using chrome stable #53.0.2785.101.
Attaching a screen cast for reference.

Following are the steps followed to reproduce the issue.
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1. Opened settings
2. Opened Search Engines window
3. Scrolled the mouse wheel up and down.
4. Observed that the search engines window scrolled smoothly without any issues.

Reporter@ - Could you please check this issue by creating a new profile without any apps and extensions and please let us know if the issue still persist or not.

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I can try another profile but I need a way to populate the search engines. Is there a file/db containing the search engines I can just copy to the other profile?

Search engines scrolls smoothly for me too, with about 15 search engines.

Reporter: how many search engines do you have?

I doubt that this is an extension issue, since extensions don't run on chrome:// pages.

Hard to say exactly how many (what's the best way to do this?), but relatively a lot, I would estimate around 150-200 or so maybe. 

I tried deleting my Chrome user folder and re-syncing everything -- the issue still appeared. 

I am able to reproduce the issue on Windows on another computer with my main profile and a new profile. I am able to see the issue after around ~50+ search engines. It gets worse as more are added. 

Thank you for providing more feedback. Adding requester "ellyjones@chromium.org" for another review and adding "Needs-Review" label for tracking.

For more details visit https://www.chromium.org/issue-tracking/autotriage - Your friendly Sheriffbot

Sounds like this is not an issue with the old Settings page, not Material Design Settings, so removing the label. If there is an issue with MD Settings, please repro on canary/dev since a lot has changed recently.

abwickes: There's a new version of that webpage which uses the "material design" UI. If you go to about://flags, you can enable it at "Enable Material Design settings". Does the problem still persist there?

Tried Material Settings on Mac and Windows. It takes a few moments to load at first, but it's much smoother. Thanks for the tip. I guess that will become the default eventually? 

Yes, that will become the default.

Seems like it's a Settings page issue that will be fixed by the MD Settings page, so closing.