The latest update (v2013.04.15.13) fixes this issue. You will need to disable filesystem protection and then go into the quarantine and restore the files. Once restored and updated, you can re-enable filesystem protection.
Just downloaded the latest update and Malwarebytes is now marking critical system files as Trojan.Downloader.ED. Running version 220.127.116.110 Build date: 4/4/2013 2:50:30 PM Database Information: Date: 4/15/2013 6:33:21 PM Database Version: v2013.04.15.12 Fingerprints loaded: 260233