I have the same problem. I disabled every extension I have in chrome and re-enabled them one by one. Only when Evernote Clipper is enabled will the up/down arrow keys stop working. PgUp/PgDn and scrolling still works.
As a workaround, I set the extension's site access to "on click" only via the extension details in Chrome:
However, if I want to actually use the web clipper, I'd have to refresh the page.