After updating Jetpack today on several of my blogs, I was notified by Wordfence of the suspected malware in wp-content/plugins/jetpack/modules/widgets/twitter.php. I didn’t save a copy of the file so I can’t tell you the exact name of the file, but I do know it contained a URL that had to do with lizamoon. I deleted the file from all the blogs that were affected (not all the updated blogs were affected which I found quite odd) and that took care of the problem.
I, too, would still like to know why a trusted plugin would have these issues. Maybe someone from Jetpack will respond?